/
SAMPL6_energyoutput_conversion_shortcutoff.txt
1710 lines (1560 loc) · 198 KB
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SAMPL6_energyoutput_conversion_shortcutoff.txt
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INFO 2018-01-01 13:44:34 Beginning InterMol conversion
INFO 2018-01-01 13:44:34 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:44:37 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:44:41 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/complex.rst7
INFO 2018-01-01 13:44:42 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/complex_converted.input
INFO 2018-01-01 13:44:42 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/complex_converted.cms
INFO 2018-01-01 13:45:14 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/complex_converted.rst7
WARNING 2018-01-01 13:45:14 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:45:14 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/complex_converted.inp
INFO 2018-01-01 13:45:16 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 578.24241215 578.24241215 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -30317.91088824 -30317.91088824
coulomb (SR) 0.00000000 -99876.03271558 -99876.03271558 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -80436.29697208 -80436.29697208
coulomb total -110746.19893120 -110751.41658766 -5.21765646 498418.91632000 609165.11525120 -104677.98260536 6068.21632584 -110746.20018640 -0.00125520 -110754.20786032 -8.00892912
coulomb-14 -11453.22971840 -11453.62628423 -0.39656583 0.00000000 11453.22971840 -11453.62673816 -0.39701976 -11453.22971840 0.00000000 0.00000000 11453.22971840
improper 0.00000000 50.22720959 50.22720959 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 50.22720456 50.22720456
proper 503.99794560 453.77084415 -50.22710145 503.99807112 0.00012552 503.99845186 0.00050626 503.99794560 0.00000000 453.80672344 -50.19122216
vdw (LR) 0.00000000 -823.94354837 -823.94354837 -565.59190664 -565.59190664 0.00000000 0.00000000 0.00000000 0.00000000 1159.82329328 1159.82329328
vdw (SR) 0.00000000 13742.35806575 13742.35806575 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 11884.85797832 11884.85797832
vdw total 13046.78603280 13047.38497937 0.59894657 12481.55143976 -565.23459304 13612.73872116 565.95268836 13046.78645120 0.00041840 13044.68127160 -2.10476120
vdw-14 128.97054480 128.97046199 -0.00008281 0.00000000 -128.97054480 128.96987076 -0.00067404 128.97054480 0.00000000 0.00000000 -128.97054480
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 893.14676480 893.14671942 -0.00004538 893.14672296 -0.00004184 893.14747190 0.00070710 893.14676480 0.00000000 893.14584432 -0.00092048
bond 169.76663680 169.76661455 -0.00002225 169.76661588 -0.00002092 169.76679077 0.00015397 169.76663680 0.00000000 169.76663680 0.00000000
bonded 1566.91134720 1566.91138772 0.00004052 1566.91140996 0.00006276 1566.91271453 0.00136733 1566.91134720 0.00000000 1566.94640912 0.03506192
dihedral 503.99794560 503.99805375 0.00010815 503.99807112 0.00012552 503.99845186 0.00050626 503.99794560 0.00000000 504.03392800 0.03598240
nonbonded -97699.41289840 -97704.03160829 -4.61870989 -97703.15716000 -3.74426160 -91065.24388420 6634.16901420 -97699.41373520 -0.00083680 -97709.52658872 -10.11369032
potential -96132.50155120 -96137.12022057 -4.61866937 -96136.24916000 -3.74760880 -96145.84349040 -13.34193920 -96132.50238800 -0.00083680 -96142.58013776 -10.07858656
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -96132.50155120
Difference in potential energy from amber=>gromacs conversion: -4.61866937
Difference in potential energy from amber=>lammps conversion: -3.74760880
Difference in potential energy from amber=>desmond conversion: -13.34193920
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -10.07858656
=======================================================================
INFO 2018-01-01 13:45:16 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/complex.rst7')
INFO 2018-01-01 13:45:16 Beginning InterMol conversion
INFO 2018-01-01 13:45:16 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:45:18 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:45:21 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/solvent.rst7
INFO 2018-01-01 13:45:22 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/solvent_converted.input
INFO 2018-01-01 13:45:22 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/solvent_converted.cms
INFO 2018-01-01 13:45:38 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/solvent_converted.rst7
WARNING 2018-01-01 13:45:38 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:45:38 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/solvent_converted.inp
INFO 2018-01-01 13:45:39 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-0/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 464.78042486 464.78042486 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -20159.16160784 -20159.16160784
coulomb (SR) 0.00000000 -89632.29331132 -89632.29331132 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -68606.87364656 -68606.87364656
coulomb total -88761.02365920 -88763.70718746 -2.68352826 413931.59260000 502692.61625920 -78153.65859646 10607.36506274 -88761.02491440 -0.00125520 -88766.03525440 -5.01159520
coulomb-14 403.79156400 403.80569900 0.01413500 0.00000000 -403.79156400 403.80576994 0.01420594 403.79156400 0.00000000 0.00000000 -403.79156400
improper 0.00000000 1.33582926 1.33582926 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.33582568 1.33582568
proper 87.01381120 85.67779161 -1.33601959 87.01362710 -0.00018410 87.01352376 -0.00028744 87.01381120 0.00000000 85.68681376 -1.32699744
vdw (LR) 0.00000000 -645.55932062 -645.55932062 -443.04982680 -443.04982680 0.00000000 0.00000000 0.00000000 0.00000000 926.87348672 926.87348672
vdw (SR) 0.00000000 11945.25617935 11945.25617935 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 10448.77231968 10448.77231968
vdw total 11376.04621520 11373.78142480 -2.26479040 10933.27462440 -442.77159080 11819.36395691 443.31774171 11376.04705200 0.00083680 11375.64580640 -0.40040880
vdw-14 74.08441440 74.08456607 0.00015167 0.00000000 -74.08441440 74.08497171 0.00055731 74.08441440 0.00000000 0.00000000 -74.08441440
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 103.85692160 103.85692084 -0.00000076 103.85692160 0.00000000 103.85666847 -0.00025313 103.85692160 0.00000000 103.85658688 -0.00033472
bond 61.22781920 61.22777870 -0.00004050 61.22777736 -0.00004184 61.22708574 -0.00073346 61.22781920 0.00000000 61.22777736 -0.00004184
bonded 252.09855200 252.09832041 -0.00023159 252.09832606 -0.00022594 252.09727797 -0.00127403 252.09855200 0.00000000 252.10700368 0.00845168
dihedral 87.01381120 87.01362087 -0.00019033 87.01362710 -0.00018410 87.01352376 -0.00028744 87.01381120 0.00000000 87.02263944 0.00882824
nonbonded -77384.97744400 -77389.92576266 -4.94831866 -77387.02969600 -2.05225200 -66334.29463956 11050.68280444 -77384.97786240 -0.00041840 -77390.38944800 -5.41200400
potential -77132.87889200 -77137.82744225 -4.94855025 -77134.93114400 -2.05225200 -77137.90136560 -5.02247360 -77132.87931040 -0.00041840 -77138.28248616 -5.40359416
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -77132.87889200
Difference in potential energy from amber=>gromacs conversion: -4.94855025
Difference in potential energy from amber=>lammps conversion: -2.05225200
Difference in potential energy from amber=>desmond conversion: -5.02247360
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -5.40359416
=======================================================================
INFO 2018-01-01 13:45:39 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-0/AMBER/solvent.rst7')
INFO 2018-01-01 13:45:40 Beginning InterMol conversion
INFO 2018-01-01 13:45:40 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:45:43 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:45:47 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/complex.rst7
INFO 2018-01-01 13:45:47 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/complex_converted.input
INFO 2018-01-01 13:45:48 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/complex_converted.cms
INFO 2018-01-01 13:46:20 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/complex_converted.rst7
WARNING 2018-01-01 13:46:20 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:46:20 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/complex_converted.inp
INFO 2018-01-01 13:46:22 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 645.59024002 645.59024002 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -29587.78422760 -29587.78422760
coulomb (SR) 0.00000000 -99032.96458556 -99032.96458556 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -80216.54103296 -80216.54103296
coulomb total -109797.90620960 -109801.16402776 -3.25781816 498026.83368000 607824.73988960 -103797.67795912 6000.22825048 -109797.90662800 -0.00041840 -109804.32526056 -6.41905096
coulomb-14 -11413.39469120 -11413.78968223 -0.39499103 0.00000000 11413.39469120 -11413.78853112 -0.39383992 -11413.39469120 0.00000000 0.00000000 11413.39469120
improper 0.00000000 75.34481811 75.34481811 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 75.34492808 75.34492808
proper 535.04071520 459.69573807 -75.34497713 535.04063152 -0.00008368 535.04012526 -0.00058994 535.04071520 0.00000000 459.73130928 -75.30940592
vdw (LR) 0.00000000 -822.55784200 -822.55784200 -564.64105080 -564.64105080 0.00000000 0.00000000 0.00000000 0.00000000 1004.56568064 1004.56568064
vdw (SR) 0.00000000 13392.06610321 13392.06610321 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 11685.53686256 11685.53686256
vdw total 12692.26776320 12693.16102197 0.89325877 12127.98360760 -564.28415560 13257.26206410 564.99430090 12692.26734480 -0.00041840 12690.10254320 -2.16522000
vdw-14 123.65268080 123.65276076 0.00007996 0.00000000 -123.65268080 123.65255026 -0.00013054 123.65268080 0.00000000 0.00000000 -123.65268080
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 920.69422080 920.69419545 -0.00002535 920.69417896 -0.00004184 920.69625841 0.00203761 920.69422080 0.00000000 920.69296560 -0.00125520
bond 190.53224720 190.53228042 0.00003322 190.53228067 0.00003347 190.52776404 -0.00448316 190.53224720 0.00000000 190.53228904 0.00004184
bonded 1646.26718320 1646.26703204 -0.00015116 1646.26709115 -0.00009205 1646.26414771 -0.00303549 1646.26718320 0.00000000 1646.30149200 0.03430880
dihedral 535.04071520 535.04055617 -0.00015903 535.04063152 -0.00008368 535.04012526 -0.00058994 535.04071520 0.00000000 535.07623736 0.03552216
nonbonded -97105.63844640 -97108.00300579 -2.36455939 -97108.08357600 -2.44512960 -90540.41589502 6565.22255138 -97105.63928320 -0.00083680 -97114.22271736 -8.58427096
potential -95459.37126320 -95461.73597375 -2.36471055 -95461.81346400 -2.44220080 -95471.14085520 -11.76959200 -95459.37210000 -0.00083680 -95467.92122536 -8.54996216
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -95459.37126320
Difference in potential energy from amber=>gromacs conversion: -2.36471055
Difference in potential energy from amber=>lammps conversion: -2.44220080
Difference in potential energy from amber=>desmond conversion: -11.76959200
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -8.54996216
=======================================================================
INFO 2018-01-01 13:46:22 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/complex.rst7')
INFO 2018-01-01 13:46:22 Beginning InterMol conversion
INFO 2018-01-01 13:46:22 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:46:24 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:46:27 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/solvent.rst7
INFO 2018-01-01 13:46:27 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/solvent_converted.input
INFO 2018-01-01 13:46:28 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/solvent_converted.cms
INFO 2018-01-01 13:46:43 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/solvent_converted.rst7
WARNING 2018-01-01 13:46:44 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:46:44 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/solvent_converted.inp
INFO 2018-01-01 13:46:45 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-1/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 453.67974368 453.67974368 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -19127.29239840 -19127.29239840
coulomb (SR) 0.00000000 -86433.58285681 -86433.58285681 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -66436.41360496 -66436.41360496
coulomb total -85558.04697600 -85561.48175523 -3.43477923 399602.08714400 485160.13412000 -75235.23827747 10322.80869853 -85558.04613920 0.00083680 -85563.70600336 -5.65902736
coulomb-14 418.40669440 418.42135791 0.01466351 0.00000000 -418.40669440 418.42130493 0.01461053 418.40669440 0.00000000 0.00000000 -418.40669440
improper 0.00000000 1.18932917 1.18932917 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.18934384 1.18934384
proper 90.64468640 89.45517399 -1.18951241 90.64450230 -0.00018410 90.64495041 0.00026401 90.64468640 0.00000000 89.46446368 -1.18022272
vdw (LR) 0.00000000 -617.38795286 -617.38795286 -423.72125304 -423.72125304 0.00000000 0.00000000 0.00000000 0.00000000 811.84796288 811.84796288
vdw (SR) 0.00000000 11713.07156767 11713.07156767 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 10360.87806936 10360.87806936
vdw total 11173.21049760 11170.88627998 -2.32421762 10749.75492856 -423.45556904 11597.19683089 423.98633329 11173.20882400 -0.00167360 11172.72603224 -0.48446536
vdw-14 75.20279760 75.20266517 -0.00013243 0.00000000 -75.20279760 75.20252857 -0.00026903 75.20279760 0.00000000 0.00000000 -75.20279760
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 152.22898240 152.22887904 -0.00010336 152.22887780 -0.00010460 152.22953260 0.00055020 152.22898240 0.00000000 152.22843848 -0.00054392
bond 46.42942960 46.42928846 -0.00014114 46.42928734 -0.00014226 46.42940324 -0.00002636 46.42942960 0.00000000 46.42930408 -0.00012552
bonded 289.30309840 289.30267066 -0.00042774 289.30266745 -0.00043095 289.30388625 0.00078785 289.30309840 0.00000000 289.31155008 0.00845168
dihedral 90.64468640 90.64450315 -0.00018325 90.64450230 -0.00018410 90.64495041 0.00026401 90.64468640 0.00000000 90.65380752 0.00912112
nonbonded -74384.83647840 -74390.59547525 -5.75899685 -74387.61632800 -2.77984960 -63638.04144658 10746.79503182 -74384.83731520 -0.00083680 -74390.97997112 -6.14349272
potential -74095.53338000 -74101.29280459 -5.75942459 -74098.31364800 -2.78026800 -74106.23605200 -10.70267200 -74095.53421680 -0.00083680 -74101.66850472 -6.13512472
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -74095.53338000
Difference in potential energy from amber=>gromacs conversion: -5.75942459
Difference in potential energy from amber=>lammps conversion: -2.78026800
Difference in potential energy from amber=>desmond conversion: -10.70267200
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -6.13512472
=======================================================================
INFO 2018-01-01 13:46:45 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-1/AMBER/solvent.rst7')
INFO 2018-01-01 13:46:46 Beginning InterMol conversion
INFO 2018-01-01 13:46:46 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:46:49 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:46:52 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/complex.rst7
INFO 2018-01-01 13:46:53 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/complex_converted.input
INFO 2018-01-01 13:46:53 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/complex_converted.cms
INFO 2018-01-01 13:47:25 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/complex_converted.rst7
WARNING 2018-01-01 13:47:26 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:47:26 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/complex_converted.inp
INFO 2018-01-01 13:47:27 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 594.18636739 594.18636739 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -29848.90833704 -29848.90833704
coulomb (SR) 0.00000000 -98512.08104071 -98512.08104071 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -79543.94826344 -79543.94826344
coulomb total -109384.19563680 -109389.72106471 -5.52542791 493637.10640000 603021.30203680 -103442.09971496 5942.09592184 -109384.19438160 0.00125520 -109392.85660048 -8.66096368
coulomb-14 -11471.42928160 -11471.82639139 -0.39710979 0.00000000 11471.42928160 -11471.82713816 -0.39785656 -11471.42928160 0.00000000 0.00000000 11471.42928160
improper 0.00000000 65.70027747 65.70027747 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 65.70038968 65.70038968
proper 539.68328160 473.98268122 -65.70060038 539.68307240 -0.00020920 539.68376276 0.00048116 539.68328160 0.00000000 474.01753544 -65.66574616
vdw (LR) 0.00000000 -820.61581473 -820.61581473 -563.30648032 -563.30648032 0.00000000 0.00000000 0.00000000 0.00000000 870.91897192 870.91897192
vdw (SR) 0.00000000 13378.29340706 13378.29340706 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 11804.97462360 11804.97462360
vdw total 12677.09239520 12677.80006181 0.70766661 12114.14197328 -562.95042192 13240.75779452 563.66539932 12677.09072160 -0.00167360 12675.89359552 -1.19879968
vdw-14 120.12264000 120.12246947 -0.00017053 0.00000000 -120.12264000 120.12244628 -0.00019372 120.12264000 0.00000000 0.00000000 -120.12264000
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 904.16742080 904.16753047 0.00010967 904.16754632 0.00012552 904.16635388 -0.00106692 904.16742080 0.00000000 904.16633296 -0.00108784
bond 209.20627600 209.20609956 -0.00017644 209.20610027 -0.00017573 209.20175100 -0.00452500 209.20627600 0.00000000 209.20610864 -0.00016736
bonded 1653.05697840 1653.05658873 -0.00038967 1653.05671899 -0.00025941 1653.05186764 -0.00511076 1653.05697840 0.00000000 1653.09036672 0.03338832
dihedral 539.68328160 539.68295869 -0.00032291 539.68307240 -0.00020920 539.68376276 0.00048116 539.68328160 0.00000000 539.71792512 0.03464352
nonbonded -96707.10324160 -96711.92100290 -4.81776130 -96711.48640000 -4.38315840 -90201.34192044 6505.76132116 -96707.10366000 -0.00041840 -96716.96300496 -9.85976336
potential -95054.04626320 -95058.86441418 -4.81815098 -95058.42984000 -4.38357680 -95064.30082880 -10.25456560 -95054.04668160 -0.00041840 -95063.87268008 -9.82641688
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -95054.04626320
Difference in potential energy from amber=>gromacs conversion: -4.81815098
Difference in potential energy from amber=>lammps conversion: -4.38357680
Difference in potential energy from amber=>desmond conversion: -10.25456560
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -9.82641688
=======================================================================
INFO 2018-01-01 13:47:27 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/complex.rst7')
INFO 2018-01-01 13:47:28 Beginning InterMol conversion
INFO 2018-01-01 13:47:28 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:47:30 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:47:32 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/solvent.rst7
INFO 2018-01-01 13:47:33 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/solvent_converted.input
INFO 2018-01-01 13:47:33 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/solvent_converted.cms
INFO 2018-01-01 13:47:49 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/solvent_converted.rst7
WARNING 2018-01-01 13:47:49 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:47:49 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/solvent_converted.inp
INFO 2018-01-01 13:47:50 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-2/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 452.09521459 452.09521459 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -18890.69481328 -18890.69481328
coulomb (SR) 0.00000000 -82259.34608266 -82259.34608266 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -62511.36596736 -62511.36596736
coulomb total -81396.08410400 -81400.18625976 -4.10215576 381014.26548000 462410.34958400 -71472.81302889 9923.27107511 -81396.08284880 0.00125520 -81402.06078064 -5.97667664
coulomb-14 407.05048160 407.06460831 0.01412671 0.00000000 -407.05048160 407.06474151 0.01425991 407.05048160 0.00000000 0.00000000 -407.05048160
improper 0.00000000 1.05224721 1.05224721 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.05223416 1.05223416
proper 79.94410640 78.89171465 -1.05239175 79.94393904 -0.00016736 79.94396833 -0.00013807 79.94410640 0.00000000 78.90074232 -1.04336408
vdw (LR) 0.00000000 -589.57192020 -589.57192020 -404.63069030 -404.63069030 0.00000000 0.00000000 0.00000000 0.00000000 988.12046864 988.12046864
vdw (SR) 0.00000000 11073.25765949 11073.25765949 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 9566.97155872 9566.97155872
vdw total 10555.14708880 10553.43078752 -1.71630128 10150.77078570 -404.37630310 10960.02942160 404.88233280 10555.14541520 -0.00167360 10555.09202736 -0.05506144
vdw-14 69.74518800 69.74504822 -0.00013978 0.00000000 -69.74518800 69.74489512 -0.00029288 69.74518800 0.00000000 0.00000000 -69.74518800
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 94.66718400 94.66738288 0.00019888 94.66738483 0.00020083 94.66767729 0.00049329 94.66718400 0.00000000 94.66710032 -0.00008368
bond 38.91412880 38.91406978 -0.00005902 38.91406981 -0.00005899 38.91449172 0.00036292 38.91412880 0.00000000 38.91408696 -0.00004184
bonded 213.52541920 213.52541452 -0.00000468 213.52539368 -0.00002552 213.52613734 0.00071814 213.52541920 0.00000000 213.53416376 0.00874456
dihedral 79.94410640 79.94396186 -0.00014454 79.94393904 -0.00016736 79.94396833 -0.00013807 79.94410640 0.00000000 79.95297648 0.00887008
nonbonded -70840.93701520 -70846.75547224 -5.81845704 -70844.09468000 -3.15766480 -60512.78360729 10328.15340791 -70840.93743360 -0.00041840 -70846.96875328 -6.03173808
potential -70627.41159600 -70633.23005772 -5.81846172 -70630.56842400 -3.15682800 -70634.48548480 -7.07388880 -70627.41201440 -0.00041840 -70633.43458952 -6.02299352
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -70627.41159600
Difference in potential energy from amber=>gromacs conversion: -5.81846172
Difference in potential energy from amber=>lammps conversion: -3.15682800
Difference in potential energy from amber=>desmond conversion: -7.07388880
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -6.02299352
=======================================================================
INFO 2018-01-01 13:47:50 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-2/AMBER/solvent.rst7')
INFO 2018-01-01 13:47:51 Beginning InterMol conversion
INFO 2018-01-01 13:47:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:47:54 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:47:58 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/complex.rst7
INFO 2018-01-01 13:47:58 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/complex_converted.input
INFO 2018-01-01 13:47:59 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/complex_converted.cms
INFO 2018-01-01 13:48:31 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/complex_converted.rst7
WARNING 2018-01-01 13:48:31 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:48:31 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/complex_converted.inp
INFO 2018-01-01 13:48:33 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 596.56057614 596.56057614 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -30092.71788296 -30092.71788296
coulomb (SR) 0.00000000 -98689.66574564 -98689.66574564 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -79376.69068776 -79376.69068776
coulomb total -109461.88247520 -109466.65610134 -4.77362614 493383.13760000 602845.02007520 -103492.64896200 5969.23351320 -109461.88163840 0.00083680 -109469.40857072 -7.52609552
coulomb-14 -11373.15716320 -11373.55093184 -0.39376864 0.00000000 11373.15716320 -11373.54983160 -0.39266840 -11373.15716320 0.00000000 0.00000000 11373.15716320
improper 0.00000000 54.47588625 54.47588625 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 54.47593104 54.47593104
proper 516.90433040 462.42823865 -54.47609175 516.90416304 -0.00016736 516.90442663 0.00009623 516.90433040 0.00000000 462.46454912 -54.43978128
vdw (LR) 0.00000000 -821.75359696 -821.75359696 -564.08641976 -564.08641976 0.00000000 0.00000000 0.00000000 0.00000000 1103.88003344 1103.88003344
vdw (SR) 0.00000000 13295.12226969 13295.12226969 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 11485.69596848 11485.69596848
vdw total 12590.91120000 12592.31879618 1.40759618 12027.18125704 -563.72994296 13155.36095288 564.44975288 12590.90994480 -0.00125520 12589.57600192 -1.33519808
vdw-14 118.95028320 118.95012345 -0.00015975 0.00000000 -118.95028320 118.94998488 -0.00029832 118.95028320 0.00000000 0.00000000 -118.95028320
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 909.08403920 909.08387270 -0.00016650 909.08387184 -0.00016736 909.08722741 0.00318821 909.08403920 0.00000000 909.08295136 -0.00108784
bond 181.58727360 181.58716672 -0.00010688 181.58716482 -0.00010878 181.58997939 0.00270579 181.58727360 0.00000000 181.58718992 -0.00008368
bonded 1607.57564320 1607.57516432 -0.00047888 1607.57519970 -0.00044350 1607.58163343 0.00599023 1607.57564320 0.00000000 1607.61062144 0.03497824
dihedral 516.90433040 516.90412490 -0.00020550 516.90416304 -0.00016736 516.90442663 0.00009623 516.90433040 0.00000000 516.94048016 0.03614976
nonbonded -96870.97127520 -96874.33730516 -3.36602996 -96874.38207200 -3.41079680 -90337.28800912 6533.68326608 -96870.97169360 -0.00041840 -96879.83256880 -8.86129360
potential -95263.39563200 -95266.76214084 -3.36650884 -95266.80977600 -3.41414400 -95274.14432800 -10.74869600 -95263.39605040 -0.00041840 -95272.22186368 -8.82623168
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -95263.39563200
Difference in potential energy from amber=>gromacs conversion: -3.36650884
Difference in potential energy from amber=>lammps conversion: -3.41414400
Difference in potential energy from amber=>desmond conversion: -10.74869600
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -8.82623168
=======================================================================
INFO 2018-01-01 13:48:33 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/complex.rst7')
INFO 2018-01-01 13:48:33 Beginning InterMol conversion
INFO 2018-01-01 13:48:33 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:48:35 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:48:38 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/solvent.rst7
INFO 2018-01-01 13:48:38 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/solvent_converted.input
INFO 2018-01-01 13:48:39 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/solvent_converted.cms
INFO 2018-01-01 13:48:54 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/solvent_converted.rst7
WARNING 2018-01-01 13:48:55 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:48:55 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/solvent_converted.inp
INFO 2018-01-01 13:48:56 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-3/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 466.95836533 466.95836533 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -20268.32919696 -20268.32919696
coulomb (SR) 0.00000000 -85992.77132938 -85992.77132938 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -64857.34832352 -64857.34832352
coulomb total -85119.42152000 -85123.76003454 -4.33851454 399396.22597600 484515.64749600 -74829.01724458 10290.40427542 -85119.42277520 -0.00125520 -85125.67752048 -6.25600048
coulomb-14 402.03888640 402.05292951 0.01404311 0.00000000 -402.03888640 402.05289862 0.01401222 402.03888640 0.00000000 0.00000000 -402.03888640
improper 0.00000000 2.29166762 2.29166762 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 2.29166048 2.29166048
proper 102.47285440 100.18123813 -2.29161627 102.47289206 0.00003766 102.47344016 0.00058576 102.47285440 0.00000000 100.19131920 -2.28153520
vdw (LR) 0.00000000 -614.84459707 -614.84459707 -421.97732000 -421.97732000 0.00000000 0.00000000 0.00000000 0.00000000 1017.18387152 1017.18387152
vdw (SR) 0.00000000 11294.47800312 11294.47800312 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 9750.99743488 9750.99743488
vdw total 10768.62732080 10766.36661855 -2.26070225 10346.91526640 -421.71205440 11190.87219379 422.24487299 10768.62773920 0.00041840 10768.18130640 -0.44601440
vdw-14 86.73306480 86.73321250 0.00014770 0.00000000 -86.73306480 86.73284179 -0.00022301 86.73306480 0.00000000 0.00000000 -86.73306480
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 116.49343840 116.49341358 -0.00002482 116.49341330 -0.00002510 116.49312711 -0.00031129 116.49343840 0.00000000 116.49302000 -0.00041840
bond 29.73861680 29.73874024 0.00012344 29.73874023 0.00012343 29.73822338 -0.00039342 29.73861680 0.00000000 29.73874232 0.00012552
bonded 248.70490960 248.70505958 0.00014998 248.70504558 0.00013598 248.70479065 -0.00011895 248.70490960 0.00000000 248.71474200 0.00983240
dihedral 102.47285440 102.47290575 0.00005135 102.47289206 0.00003766 102.47344016 0.00058576 102.47285440 0.00000000 102.48297968 0.01012528
nonbonded -74350.79419920 -74357.39341599 -6.59921679 -74354.06901600 -3.27481680 -63638.14505079 10712.64914841 -74350.79503600 -0.00083680 -74357.49621408 -6.70201488
potential -74102.08928960 -74108.68835641 -6.59906681 -74105.36368800 -3.27439840 -74109.60459040 -7.51530080 -74102.09012640 -0.00083680 -74108.78151392 -6.69222432
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -74102.08928960
Difference in potential energy from amber=>gromacs conversion: -6.59906681
Difference in potential energy from amber=>lammps conversion: -3.27439840
Difference in potential energy from amber=>desmond conversion: -7.51530080
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -6.69222432
=======================================================================
INFO 2018-01-01 13:48:56 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-3/AMBER/solvent.rst7')
INFO 2018-01-01 13:48:56 Beginning InterMol conversion
INFO 2018-01-01 13:48:56 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:49:00 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:49:04 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/complex.rst7
INFO 2018-01-01 13:49:04 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/complex_converted.input
INFO 2018-01-01 13:49:05 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/complex_converted.cms
INFO 2018-01-01 13:49:37 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/complex_converted.rst7
WARNING 2018-01-01 13:49:37 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:49:37 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/complex_converted.inp
INFO 2018-01-01 13:49:39 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 545.29366088 545.29366088 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -30048.80094536 -30048.80094536
coulomb (SR) 0.00000000 -99969.60030716 -99969.60030716 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -80866.69371344 -80866.69371344
coulomb total -110906.08714400 -110912.51737900 -6.43023500 498542.72088000 609448.80802400 -104801.29073376 6104.79641024 -110906.08672560 0.00041840 -110915.49465880 -9.40751480
coulomb-14 -11487.81298880 -11488.21073272 -0.39774392 0.00000000 11487.81298880 -11488.21063616 -0.39764736 -11487.81298880 0.00000000 0.00000000 11487.81298880
improper 0.00000000 50.95306129 50.95306129 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 50.95304488 50.95304488
proper 496.11612640 445.16300001 -50.95312639 496.11604272 -0.00008368 496.11536073 -0.00076567 496.11612640 0.00000000 445.19889656 -50.91722984
vdw (LR) 0.00000000 -820.03277279 -820.03277279 -562.91092496 -562.91092496 0.00000000 0.00000000 0.00000000 0.00000000 1148.46298016 1148.46298016
vdw (SR) 0.00000000 13929.88262028 13929.88262028 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 12096.35286048 12096.35286048
vdw total 13245.99003840 13247.53078551 1.54074711 12683.43475344 -562.55528496 13809.27507823 563.28503983 13245.98920160 -0.00083680 13244.81584064 -1.17419776
vdw-14 137.68079600 137.68093802 0.00014202 0.00000000 -137.68079600 137.68065207 -0.00014393 137.68079600 0.00000000 0.00000000 -137.68079600
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 983.90609280 983.90619569 0.00010289 983.90617648 0.00008368 983.90389202 -0.00220078 983.90609280 0.00000000 983.90513048 -0.00096232
bond 196.61076240 196.61062867 -0.00013373 196.61062851 -0.00013389 196.60895868 -0.00180372 196.61076240 0.00000000 196.61063688 -0.00012552
bonded 1676.63298160 1676.63288566 -0.00009594 1676.63284771 -0.00013389 1676.62821142 -0.00477018 1676.63298160 0.00000000 1676.66770880 0.03472720
dihedral 496.11612640 496.11606130 -0.00006510 496.11604272 -0.00008368 496.11536073 -0.00076567 496.11612640 0.00000000 496.15194144 0.03581504
nonbonded -97660.09710560 -97664.98659348 -4.88948788 -97665.13296800 -5.03586240 -90992.01565553 6668.08145007 -97660.09752400 -0.00041840 -97670.67881816 -10.58171256
potential -95983.46412400 -95988.35370782 -4.88958382 -95988.49956800 -5.03544400 -95994.42160160 -10.95747760 -95983.46454240 -0.00041840 -95994.01110936 -10.54698536
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -95983.46412400
Difference in potential energy from amber=>gromacs conversion: -4.88958382
Difference in potential energy from amber=>lammps conversion: -5.03544400
Difference in potential energy from amber=>desmond conversion: -10.95747760
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -10.54698536
=======================================================================
INFO 2018-01-01 13:49:39 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/complex.rst7')
INFO 2018-01-01 13:49:39 Beginning InterMol conversion
INFO 2018-01-01 13:49:39 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:49:42 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:49:44 Evaluating energy of SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/solvent.rst7
INFO 2018-01-01 13:49:45 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/solvent_converted.input
INFO 2018-01-01 13:49:45 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/solvent_converted.cms
INFO 2018-01-01 13:50:01 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/solvent_converted.rst7
WARNING 2018-01-01 13:50:01 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:50:01 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/solvent_converted.inp
INFO 2018-01-01 13:50:03 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_CB8-G3-4/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 493.19340230 493.19340230 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -20196.80396800 -20196.80396800
coulomb (SR) 0.00000000 -91563.63090894 -91563.63090894 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -70494.24500128 -70494.24500128
coulomb total -90687.16446000 -90688.76933582 -1.60487582 422909.30600000 513596.47046000 -79930.65235219 10756.51210781 -90687.16571520 -0.00125520 -90691.04896928 -3.88450928
coulomb-14 381.65485680 381.66817083 0.01331403 0.00000000 -381.65485680 381.66822301 0.01336621 381.65485680 0.00000000 0.00000000 -381.65485680
improper 0.00000000 1.33432711 1.33432711 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.33431944 1.33431944
proper 106.61543280 105.28121015 -1.33422265 106.61549556 0.00006276 106.61572652 0.00029372 106.61543280 0.00000000 105.29052736 -1.32490544
vdw (LR) 0.00000000 -657.17655306 -657.17655306 -451.02469816 -451.02469816 0.00000000 0.00000000 0.00000000 0.00000000 890.88284424 890.88284424
vdw (SR) 0.00000000 11903.93568388 11903.93568388 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 10436.98645192 10436.98645192
vdw total 11328.29464160 11325.98411467 -2.31052693 10877.55278184 -450.74185976 11779.60428731 451.30964571 11328.29506000 0.00041840 11327.86929616 -0.42534544
vdw-14 79.22487680 79.22498385 0.00010705 0.00000000 -79.22487680 79.22501947 0.00014267 79.22487680 0.00000000 0.00000000 -79.22487680
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 106.77107760 106.77119045 0.00011285 106.77119057 0.00011297 106.77252736 0.00144976 106.77107760 0.00000000 106.77078472 -0.00029288
bond 42.15045280 42.15039969 -0.00005311 42.15039841 -0.00005439 42.15086451 0.00041171 42.15045280 0.00000000 42.15041096 -0.00004184
bonded 255.53696320 255.53712739 0.00016419 255.53708454 0.00012134 255.53911838 0.00215518 255.53696320 0.00000000 255.54604248 0.00907928
dihedral 106.61543280 106.61553726 0.00010446 106.61549556 0.00006276 106.61572652 0.00029372 106.61543280 0.00000000 106.62484680 0.00941400
nonbonded -79358.86981840 -79362.78522115 -3.91540275 -79360.05347200 -1.18365360 -68151.04806488 11207.82175352 -79358.87065520 -0.00083680 -79363.17967312 -4.30985472
potential -79103.33285520 -79107.24809375 -3.91523855 -79104.51567200 -1.18281680 -79110.88120960 -7.54835440 -79103.33369200 -0.00083680 -79107.63358880 -4.30073360
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -79103.33285520
Difference in potential energy from amber=>gromacs conversion: -3.91523855
Difference in potential energy from amber=>lammps conversion: -1.18281680
Difference in potential energy from amber=>desmond conversion: -7.54835440
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -4.30073360
=======================================================================
INFO 2018-01-01 13:50:03 Finished!
('SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/CB8-G3-4/AMBER/solvent.rst7')
INFO 2018-01-01 13:50:03 Beginning InterMol conversion
INFO 2018-01-01 13:50:03 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:50:06 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:50:11 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/complex.rst7
INFO 2018-01-01 13:50:11 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/complex_converted.input
INFO 2018-01-01 13:50:12 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/complex_converted.cms
INFO 2018-01-01 13:50:44 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/complex_converted.rst7
WARNING 2018-01-01 13:50:44 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:50:44 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/complex_converted.inp
INFO 2018-01-01 13:50:46 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 749.32424955 749.32424955 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -29178.76429536 -29178.76429536
coulomb (SR) 0.00000000 -130364.97348404 -130364.97348404 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -100166.41808216 -100166.41808216
coulomb total -129336.85985760 -129341.51041237 -4.65055477 589571.33112000 718908.19097760 -112249.88515902 17086.97469858 -129336.85358160 0.00627600 -129345.18237752 -8.32251992
coulomb-14 274.12940400 274.13882213 0.00941813 0.00000000 -274.12940400 274.13930418 0.00990018 274.12940400 0.00000000 0.00000000 -274.12940400
improper 0.00000000 17.65597281 17.65597281 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 17.65597792 17.65597792
proper 564.66510880 547.00892605 -17.65618275 564.66489960 -0.00020920 564.66473224 -0.00037656 564.66510880 0.00000000 547.00473768 -17.66037112
vdw (LR) 0.00000000 -969.47827674 -969.47827674 -665.41913416 -665.41913416 0.00000000 0.00000000 0.00000000 0.00000000 1056.87082696 1056.87082696
vdw (SR) 0.00000000 16173.32425297 16173.32425297 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14470.19588688 14470.19588688
vdw total 15529.38502640 15528.21033562 -1.17469078 14864.38052664 -665.00449976 16195.23000431 665.84497791 15529.38251600 -0.00251040 15527.06671384 -2.31831256
vdw-14 324.36418160 324.36435940 0.00017780 0.00000000 -324.36418160 324.36438703 0.00020543 324.36418160 0.00000000 0.00000000 -324.36418160
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 490.41333440 490.41320823 -0.00012617 490.41320888 -0.00012552 490.41243066 -0.00090374 490.41333440 0.00000000 490.41166080 -0.00167360
bond 262.78992720 262.79009242 0.00016522 262.79009038 0.00016318 262.78950001 -0.00042719 262.78992720 0.00000000 262.79009456 0.00016736
bonded 1317.86837040 1317.86819951 -0.00017089 1317.86819886 -0.00017154 1317.86666291 -0.00170749 1317.86837040 0.00000000 1317.86247096 -0.00589944
dihedral 564.66510880 564.66489886 -0.00020994 564.66489960 -0.00020920 564.66473224 -0.00037656 564.66510880 0.00000000 564.66071560 -0.00439320
nonbonded -113807.47483120 -113813.30007674 -5.82524554 -113810.73291200 -3.25808080 -96054.65515470 17752.81967650 -113807.47106560 0.00376560 -113818.11566368 -10.64083248
potential -112489.60646080 -112495.43187723 -5.82541643 -112492.86496000 -3.25849920 -112500.06980800 -10.46334720 -112489.60269520 0.00376560 -112500.25327640 -10.64681560
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -112489.60646080
Difference in potential energy from amber=>gromacs conversion: -5.82541643
Difference in potential energy from amber=>lammps conversion: -3.25849920
Difference in potential energy from amber=>desmond conversion: -10.46334720
Difference in potential energy from amber=>amber conversion: 0.00376560
Difference in potential energy from amber=>charmm conversion: -10.64681560
=======================================================================
INFO 2018-01-01 13:50:46 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/complex.rst7')
INFO 2018-01-01 13:50:47 Beginning InterMol conversion
INFO 2018-01-01 13:50:47 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:50:48 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:50:49 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/solvent.rst7
INFO 2018-01-01 13:50:49 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/solvent_converted.input
INFO 2018-01-01 13:50:50 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/solvent_converted.cms
INFO 2018-01-01 13:51:05 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/solvent_converted.rst7
WARNING 2018-01-01 13:51:05 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:51:05 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/solvent_converted.inp
INFO 2018-01-01 13:51:06 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-0/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 253.05933814 253.05933814 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -11679.16115784 -11679.16115784
coulomb (SR) 0.00000000 -46979.25238150 -46979.25238150 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -35051.16138792 -35051.16138792
coulomb total -46727.29525440 -46729.37642548 -2.08117108 224569.66459200 271296.95984640 -41723.07124552 5004.22400888 -46727.29734640 -0.00209200 -46730.32254576 -3.02729136
coulomb-14 -3.18318720 -3.18338212 -0.00019492 0.00000000 3.18318720 -3.18338368 -0.00019648 -3.18318720 0.00000000 0.00000000 3.18318720
improper 0.00000000 0.18913261 0.18913261 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.18911680 0.18911680
proper 31.39715440 31.20810898 -0.18904542 31.39724770 0.00009330 31.39728214 0.00012774 31.39715440 0.00000000 31.20824680 -0.18890760
vdw (LR) 0.00000000 -342.17539078 -342.17539078 -234.83393289 -234.83393289 0.00000000 0.00000000 0.00000000 0.00000000 712.43114392 712.43114392
vdw (SR) 0.00000000 6190.58238897 6190.58238897 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5143.35463184 5143.35463184
vdw total 5855.46030240 5854.79601354 -0.66428886 5620.77155431 -234.68874809 6090.44155677 234.98125437 5855.46197600 0.00167360 5855.78577576 0.32547336
vdw-14 6.38896800 6.38901534 0.00004734 0.00000000 -6.38896800 6.38895829 -0.00000971 6.38896800 0.00000000 0.00000000 -6.38896800
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 32.53311040 32.53306033 -0.00005007 32.53306019 -0.00005021 32.53295831 -0.00015209 32.53311040 0.00000000 32.53285936 -0.00025104
bond 8.61987680 8.61984987 -0.00002693 8.61985002 -0.00002678 8.62009223 0.00021543 8.61987680 0.00000000 8.61983496 -0.00004184
bonded 72.55014160 72.55015180 0.00001020 72.55015792 0.00001632 72.55033268 0.00019108 72.55014160 0.00000000 72.55005792 -0.00008368
dihedral 31.39715440 31.39724159 0.00008719 31.39724770 0.00009330 31.39728214 0.00012774 31.39715440 0.00000000 31.39736360 0.00020920
nonbonded -40871.83495200 -40874.58041195 -2.74545995 -40873.45792560 -1.62297360 -35632.62968875 5239.20526325 -40871.83537040 -0.00041840 -40874.53677000 -2.70181800
potential -40799.28481040 -40802.03026015 -2.74544975 -40800.90778400 -1.62297360 -40802.66380880 -3.37899840 -40799.28522880 -0.00041840 -40801.98662840 -2.70181800
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -40799.28481040
Difference in potential energy from amber=>gromacs conversion: -2.74544975
Difference in potential energy from amber=>lammps conversion: -1.62297360
Difference in potential energy from amber=>desmond conversion: -3.37899840
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -2.70181800
=======================================================================
INFO 2018-01-01 13:51:06 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-0/AMBER/solvent.rst7')
INFO 2018-01-01 13:51:07 Beginning InterMol conversion
INFO 2018-01-01 13:51:07 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:51:10 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:51:14 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/complex.rst7
INFO 2018-01-01 13:51:15 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/complex_converted.input
INFO 2018-01-01 13:51:16 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/complex_converted.cms
INFO 2018-01-01 13:51:48 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/complex_converted.rst7
WARNING 2018-01-01 13:51:48 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:51:48 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/complex_converted.inp
INFO 2018-01-01 13:51:50 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 712.74439756 712.74439756 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -29447.18241384 -29447.18241384
coulomb (SR) 0.00000000 -130651.04632745 -130651.04632745 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -100259.04046168 -100259.04046168
coulomb total -129696.44118560 -129702.27937143 -5.83818583 589905.42352000 719601.86470560 -112593.70546655 17102.73571905 -129696.44244080 -0.00125520 -129706.22287552 -9.78168992
coulomb-14 236.01441920 236.02255846 0.00813926 0.00000000 -236.01441920 236.02295665 0.00853745 236.01441920 0.00000000 0.00000000 -236.01441920
improper 0.00000000 16.21957550 16.21957550 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 16.21956888 16.21956888
proper 549.06171760 532.84203475 -16.21968285 549.06159208 -0.00012552 549.06248746 0.00076986 549.06171760 0.00000000 532.83855048 -16.22316712
vdw (LR) 0.00000000 -980.70975841 -980.70975841 -673.11874016 -673.11874016 0.00000000 0.00000000 0.00000000 0.00000000 1089.90798384 1089.90798384
vdw (SR) 0.00000000 16366.89336766 16366.89336766 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14607.14063360 14607.14063360
vdw total 15699.31693120 15698.50301929 -0.81391191 15026.61784624 -672.69908496 16372.86996554 673.55303434 15699.31734960 0.00041840 15697.04861744 -2.26831376
vdw-14 312.31928240 312.31941004 0.00012764 0.00000000 -312.31928240 312.31977946 0.00049706 312.31928240 0.00000000 0.00000000 -312.31928240
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 404.41539840 404.41556031 0.00016191 404.41556158 0.00016318 404.41542016 0.00002176 404.41539840 0.00000000 404.41385032 -0.00154808
bond 197.01661040 197.01656905 -0.00004135 197.01656856 -0.00004184 197.01466275 -0.00194765 197.01661040 0.00000000 197.01656856 -0.00004184
bonded 1150.49372640 1150.49373962 0.00001322 1150.49372222 -0.00000418 1150.49257036 -0.00115604 1150.49372640 0.00000000 1150.48853824 -0.00518816
dihedral 549.06171760 549.06161025 -0.00010735 549.06159208 -0.00012552 549.06248746 0.00076986 549.06171760 0.00000000 549.05811936 -0.00359824
nonbonded -113997.12425440 -114003.77635214 -6.65209774 -114001.26390400 -4.13964960 -96220.83550101 17776.28875339 -113997.12509120 -0.00083680 -114009.17425808 -12.05000368
potential -112846.63052800 -112853.28261252 -6.65208452 -112850.76850400 -4.13797600 -112856.70978400 -10.07925600 -112846.63136480 -0.00083680 -112858.68576168 -12.05523368
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -112846.63052800
Difference in potential energy from amber=>gromacs conversion: -6.65208452
Difference in potential energy from amber=>lammps conversion: -4.13797600
Difference in potential energy from amber=>desmond conversion: -10.07925600
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -12.05523368
=======================================================================
INFO 2018-01-01 13:51:50 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/complex.rst7')
INFO 2018-01-01 13:51:51 Beginning InterMol conversion
INFO 2018-01-01 13:51:51 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:51:52 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:51:53 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/solvent.rst7
INFO 2018-01-01 13:51:54 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/solvent_converted.input
INFO 2018-01-01 13:51:54 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/solvent_converted.cms
INFO 2018-01-01 13:52:09 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/solvent_converted.rst7
WARNING 2018-01-01 13:52:10 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:52:10 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/solvent_converted.inp
INFO 2018-01-01 13:52:11 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-1/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 210.70053200 210.70053200 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -11397.89690416 -11397.89690416
coulomb (SR) 0.00000000 -46906.47581535 -46906.47581535 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -35299.87960264 -35299.87960264
coulomb total -46694.31278240 -46696.80120572 -2.48842332 224793.21571200 271487.52849440 -41643.99932480 5050.31345760 -46694.31278240 0.00000000 -46697.77650680 -3.46372440
coulomb-14 -1.02591680 -1.02592237 -0.00000557 0.00000000 1.02591680 -1.02593496 -0.00001816 -1.02591680 0.00000000 0.00000000 1.02591680
improper 0.00000000 1.04817012 1.04817012 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.04817568 1.04817568
proper 35.49496400 34.44683024 -1.04813376 35.49502090 0.00005690 35.49536466 0.00040066 35.49496400 0.00000000 34.44712304 -1.04784096
vdw (LR) 0.00000000 -344.42384093 -344.42384093 -236.37519297 -236.37519297 0.00000000 0.00000000 0.00000000 0.00000000 558.43525832 558.43525832
vdw (SR) 0.00000000 6264.12928418 6264.12928418 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5368.00062096 5368.00062096
vdw total 5926.31215840 5925.43558996 -0.87656844 5690.08298703 -236.22917137 6162.84045079 236.52829239 5926.31174000 -0.00041840 5926.43587928 0.12372088
vdw-14 5.72998800 5.73014670 0.00015870 0.00000000 -5.72998800 5.73014967 0.00016167 5.72998800 0.00000000 0.00000000 -5.72998800
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 30.27165840 30.27178618 0.00012778 30.27178601 0.00012761 30.27186287 0.00020447 30.27165840 0.00000000 30.27157472 -0.00008368
bond 7.54877280 7.54885108 0.00007828 7.54885104 0.00007824 7.54913129 0.00035849 7.54877280 0.00000000 7.54885648 0.00008368
bonded 73.31539520 73.31563763 0.00024243 73.31565796 0.00026276 73.31635882 0.00096362 73.31539520 0.00000000 73.31572992 0.00033472
dihedral 35.49496400 35.49500036 0.00003636 35.49502090 0.00005690 35.49536466 0.00040066 35.49496400 0.00000000 35.49529872 0.00033472
nonbonded -40768.00062400 -40771.36561576 -3.36499176 -40770.01312800 -2.01250400 -35481.15887401 5286.84174999 -40768.00104240 -0.00041840 -40771.34062752 -3.34000352
potential -40694.68522880 -40698.04997814 -3.36474934 -40696.69731440 -2.01208560 -40698.48020048 -3.79497168 -40694.68564720 -0.00041840 -40698.02485576 -3.33962696
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -40694.68522880
Difference in potential energy from amber=>gromacs conversion: -3.36474934
Difference in potential energy from amber=>lammps conversion: -2.01208560
Difference in potential energy from amber=>desmond conversion: -3.79497168
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -3.33962696
=======================================================================
INFO 2018-01-01 13:52:11 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-1/AMBER/solvent.rst7')
INFO 2018-01-01 13:52:11 Beginning InterMol conversion
INFO 2018-01-01 13:52:11 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:52:14 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:52:19 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/complex.rst7
INFO 2018-01-01 13:52:19 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/complex_converted.input
INFO 2018-01-01 13:52:20 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/complex_converted.cms
INFO 2018-01-01 13:52:52 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/complex_converted.rst7
WARNING 2018-01-01 13:52:52 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:52:52 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/complex_converted.inp
INFO 2018-01-01 13:52:54 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 715.24784654 715.24784654 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -30380.41516216 -30380.41516216
coulomb (SR) 0.00000000 -131954.67710613 -131954.67710613 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -100578.87805736 -100578.87805736
coulomb total -130947.58479760 -130955.72290639 -8.13810879 588542.10896000 719489.69375760 -113823.82086776 17123.76392984 -130947.58437920 0.00041840 -130959.29321952 -11.70842192
coulomb-14 283.69653840 283.70635321 0.00981481 0.00000000 -283.69653840 283.70617624 0.00963784 283.69653840 0.00000000 0.00000000 -283.69653840
improper 0.00000000 15.81605059 15.81605059 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 15.81602208 15.81602208
proper 588.49006000 572.67422860 -15.81583140 588.49022736 0.00016736 588.49076291 0.00070291 588.49006000 0.00000000 572.67089992 -15.81916008
vdw (LR) 0.00000000 -978.81583960 -978.81583960 -671.82040312 -671.82040312 0.00000000 0.00000000 0.00000000 0.00000000 1305.87254952 1305.87254952
vdw (SR) 0.00000000 16794.05664674 16794.05664674 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 14849.07717008 14849.07717008
vdw total 16157.45112400 16156.35129879 -1.09982521 15486.04912088 -671.40200312 16829.69785454 672.24673054 16157.44986880 -0.00125520 16154.94971960 -2.50140440
vdw-14 341.11064160 341.11049164 -0.00014996 0.00000000 -341.11064160 341.11032654 -0.00031506 341.11064160 0.00000000 0.00000000 -341.11064160
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 382.85817520 382.85824877 0.00007357 382.85825051 0.00007531 382.85938856 0.00121336 382.85817520 0.00000000 382.85662712 -0.00154808
bond 178.72165200 178.72143696 -0.00021504 178.72143862 -0.00021338 178.72095997 -0.00069203 178.72165200 0.00000000 178.72144280 -0.00020920
bonded 1150.06988720 1150.06996493 0.00007773 1150.06991649 0.00002929 1150.07111144 0.00122424 1150.06988720 0.00000000 1150.06499192 -0.00489528
dihedral 588.49006000 588.49027919 0.00021919 588.49022736 0.00016736 588.49076291 0.00070291 588.49006000 0.00000000 588.48692200 -0.00313800
nonbonded -114790.13367360 -114799.37160760 -9.23793400 -114796.06072800 -5.92705440 -96994.12301321 17796.01066039 -114790.13451040 -0.00083680 -114804.34349992 -14.20982632
potential -113640.06378640 -113649.30164267 -9.23785627 -113645.99209600 -5.92830960 -113652.71578400 -12.65199760 -113640.06462320 -0.00083680 -113654.27846616 -14.21467976
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -113640.06378640
Difference in potential energy from amber=>gromacs conversion: -9.23785627
Difference in potential energy from amber=>lammps conversion: -5.92830960
Difference in potential energy from amber=>desmond conversion: -12.65199760
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -14.21467976
=======================================================================
INFO 2018-01-01 13:52:54 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/complex.rst7')
INFO 2018-01-01 13:52:55 Beginning InterMol conversion
INFO 2018-01-01 13:52:55 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:52:56 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:52:57 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/solvent.rst7
INFO 2018-01-01 13:52:57 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/solvent_converted.input
INFO 2018-01-01 13:52:58 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/solvent_converted.cms
INFO 2018-01-01 13:53:13 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/solvent_converted.rst7
WARNING 2018-01-01 13:53:13 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:53:13 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/solvent_converted.inp
INFO 2018-01-01 13:53:14 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-2/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 250.93289444 250.93289444 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -11263.85957720 -11263.85957720
coulomb (SR) 0.00000000 -47018.99488003 -47018.99488003 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -35507.08898096 -35507.08898096
coulomb total -46767.81269200 -46770.14360983 -2.33091783 224567.34247200 271335.15516400 -41760.35253166 5007.46016034 -46767.81352880 -0.00083680 -46770.94855816 -3.13586616
coulomb-14 -2.08154000 -2.08162425 -0.00008425 0.00000000 2.08154000 -2.08161614 -0.00007614 -2.08154000 0.00000000 0.00000000 2.08154000
improper 0.00000000 1.30058352 1.30058352 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 1.30059640 1.30059640
proper 35.19831840 33.89771404 -1.30060436 35.19829120 -0.00002720 35.19837359 0.00005519 35.19831840 0.00000000 33.89780568 -1.30051272
vdw (LR) 0.00000000 -342.88526566 -342.88526566 -235.32054046 -235.32054046 0.00000000 0.00000000 0.00000000 0.00000000 612.23250272 612.23250272
vdw (SR) 0.00000000 6378.41885457 6378.41885457 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 5429.32563448 5429.32563448
vdw total 6041.45709360 6040.65650793 -0.80058567 5806.28173794 -235.17535566 6276.92017695 235.46308335 6041.45751200 0.00041840 6041.55813720 0.10104360
vdw-14 5.12288960 5.12291902 0.00002942 0.00000000 -5.12288960 5.12292127 0.00003167 5.12288960 0.00000000 0.00000000 -5.12288960
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 45.51522560 45.51531605 0.00009045 45.51531765 0.00009205 45.51513104 -0.00009456 45.51522560 0.00000000 45.51510008 -0.00012552
bond 10.47464400 10.47451882 -0.00012518 10.47451890 -0.00012510 10.47347210 -0.00117190 10.47464400 0.00000000 10.47451848 -0.00012552
bonded 91.18818800 91.18813244 -0.00005556 91.18812775 -0.00006025 91.18697673 -0.00121127 91.18818800 0.00000000 91.18802064 -0.00016736
dihedral 35.19831840 35.19829756 -0.00002084 35.19829120 -0.00002720 35.19837359 0.00005519 35.19831840 0.00000000 35.19840208 0.00008368
nonbonded -40726.35559840 -40729.48710190 -3.13150350 -40728.04384240 -1.68824400 -35483.43235470 5242.92324370 -40726.35601680 -0.00041840 -40729.39042096 -3.03482256
potential -40635.16741040 -40638.29896947 -3.13155907 -40636.85607280 -1.68866240 -40638.83267808 -3.66526768 -40635.16782880 -0.00041840 -40638.20244216 -3.03503176
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -40635.16741040
Difference in potential energy from amber=>gromacs conversion: -3.13155907
Difference in potential energy from amber=>lammps conversion: -1.68866240
Difference in potential energy from amber=>desmond conversion: -3.66526768
Difference in potential energy from amber=>amber conversion: -0.00041840
Difference in potential energy from amber=>charmm conversion: -3.03503176
=======================================================================
INFO 2018-01-01 13:53:14 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/solvent.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-2/AMBER/solvent.rst7')
INFO 2018-01-01 13:53:15 Beginning InterMol conversion
INFO 2018-01-01 13:53:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:53:18 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:53:22 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-3/AMBER/complex.rst7
INFO 2018-01-01 13:53:23 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/complex_converted.input
INFO 2018-01-01 13:53:24 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/complex_converted.cms
INFO 2018-01-01 13:53:55 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/complex_converted.rst7
WARNING 2018-01-01 13:53:56 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:53:56 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/complex_converted.inp
INFO 2018-01-01 13:53:58 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-3/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/complex_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 691.52933021 691.52933021 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -30181.28165696 -30181.28165696
coulomb (SR) 0.00000000 -130327.86599756 -130327.86599756 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -99192.15154880 -99192.15154880
coulomb total -129362.86885680 -129369.52494113 -6.65608433 590034.79280000 719397.66165680 -112213.31686932 17149.55198748 -129362.86969360 -0.00083680 -129373.43320576 -10.56434896
coulomb-14 266.80238320 266.81172622 0.00934302 0.00000000 -266.80238320 266.81115788 0.00877468 266.80238320 0.00000000 0.00000000 -266.80238320
improper 0.00000000 18.96067637 18.96067637 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 18.96067464 18.96067464
proper 597.13253040 578.17206396 -18.96046644 597.13273960 0.00020920 597.13241325 -0.00011715 597.13253040 0.00000000 578.16825752 -18.96427288
vdw (LR) 0.00000000 -976.77115891 -976.77115891 -670.41867944 -670.41867944 0.00000000 0.00000000 0.00000000 0.00000000 1287.59047784 1287.59047784
vdw (SR) 0.00000000 15915.71516193 15915.71516193 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 13944.13144160 13944.13144160
vdw total 15233.34652480 15232.52213527 -0.82438953 14563.34540856 -670.00111624 15904.18482639 670.83830159 15233.34652480 0.00000000 15231.72191944 -1.62460536
vdw-14 293.57830960 293.57813225 -0.00017735 0.00000000 -293.57830960 293.57836023 0.00005063 293.57830960 0.00000000 0.00000000 -293.57830960
-----------------------------------------------------------------------
Comparable energy terms: these should be very close
-----------------------------------------------------------------------
angle 462.86755200 462.86741202 -0.00013998 462.86742648 -0.00012552 462.86719218 -0.00035982 462.86755200 0.00000000 462.86587840 -0.00167360
bond 206.34232800 206.34246872 0.00014072 206.34247026 0.00014226 206.34326271 0.00093471 206.34232800 0.00000000 206.34249536 0.00016736
bonded 1266.34241040 1266.34262108 0.00021068 1266.34263634 0.00022594 1266.34286813 0.00045773 1266.34241040 0.00000000 1266.33730592 -0.00510448
dihedral 597.13253040 597.13274033 0.00020993 597.13273960 0.00020920 597.13241325 -0.00011715 597.13253040 0.00000000 597.12893216 -0.00359824
nonbonded -114129.52233200 -114137.00280586 -7.48047386 -114134.70840000 -5.18606800 -96309.13204293 17820.39028907 -114129.52316880 -0.00083680 -114141.71128632 -12.18895432
potential -112863.17992160 -112870.66018478 -7.48026318 -112868.36222400 -5.18230240 -112873.83489600 -10.65497440 -112863.18075840 -0.00083680 -112875.37402224 -12.19410064
---------------- Total Potential Energy Comparison --------------------
Input amber potential energy: -112863.17992160
Difference in potential energy from amber=>gromacs conversion: -7.48026318
Difference in potential energy from amber=>lammps conversion: -5.18230240
Difference in potential energy from amber=>desmond conversion: -10.65497440
Difference in potential energy from amber=>amber conversion: -0.00083680
Difference in potential energy from amber=>charmm conversion: -12.19410064
=======================================================================
INFO 2018-01-01 13:53:58 Finished!
('SAMPL6/host_guest/SAMPLing/OA-G3-3/AMBER/complex.prmtop', 'SAMPL6/host_guest/SAMPLing/OA-G3-3/AMBER/complex.rst7')
INFO 2018-01-01 13:53:58 Beginning InterMol conversion
INFO 2018-01-01 13:53:58 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
WARNING 2018-01-01 13:53:59 MacroModel atom type is not defined in other files, is set to 1 for all cases as it must be validly defined for desmond files to run. However, it does not affect the energies.
INFO 2018-01-01 13:54:01 Evaluating energy of SAMPL6/host_guest/SAMPLing/OA-G3-3/AMBER/solvent.rst7
INFO 2018-01-01 13:54:01 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/solvent_converted.input
INFO 2018-01-01 13:54:01 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/solvent_converted.cms
INFO 2018-01-01 13:54:17 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/solvent_converted.rst7
WARNING 2018-01-01 13:54:17 CHARMM energy input file not used, information recreated from command line options
INFO 2018-01-01 13:54:17 Evaluating energy of SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/solvent_converted.inp
INFO 2018-01-01 13:54:18 InterMol Conversion Energy Comparison Results
amber input energy file: SAMPL6/host_guest/SAMPLing/OA-G3-3/AMBER/amber.out
gromacs output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/energy.xvg
lammps output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/lammps_stdout.txt
desmond output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/solvent_converted.enegrp.dat
amber output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/amber.out
charmm output energy file: SAMPL6/host_guest/SAMPLing/converted_OA-G3-3/charmm_stdout.txt
Energy group summary
=======================================================================
type input(amber) output (gromacs) diff (gromacs) output (lammps) diff (lammps) output (desmond) diff (desmond) output (amber) diff (amber) output (charmm) diff (charmm)
-----------------------------------------------------------------------
Not comparable energies: are likely not to be the same
-----------------------------------------------------------------------
coulomb (LR) 0.00000000 232.60593440 232.60593440 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -11637.14078560 -11637.14078560
coulomb (SR) 0.00000000 -46856.20675752 -46856.20675752 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 0.00000000 -34981.98300640 -34981.98300640
coulomb total -46615.61048720 -46618.27524620 -2.66475900 224596.33340800 271211.94389520 -41585.31878927 5030.29169793 -46615.60839520 0.00209200 -46619.12379200 -3.51330480
coulomb-14 5.32539520 5.32557693 0.00018173 0.00000000 -5.32539520 5.32556361 0.00016841 5.32539520 0.00000000 0.00000000 -5.32539520