continue improving tutorial 3

files/tutorial3/mergePEGH2O/input.lmp

@@ -0,0 +1,45 @@
+
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+pair_style lj/cut/coul/long 10
+kspace_style pppm 1e-5
+special_bonds lj 0.0 0.0 0.5 coul 0.0 0.0 1.0 &
+angle yes dihedral yes
+
+read_data ../pureH2O/H2O.data &
+    extra/bond/per/atom 3 &
+    extra/angle/per/atom 6 &
+    extra/dihedral/per/atom 10 &
+    extra/special/per/atom 14
+include ../PARM.lmp
+
+molecule pegmol PEG-GROMOS.mol
+create_atoms 0 single 0 0 0 mol pegmol 454756
+
+group H2O type OW HW
+group PEG type C CPos H HC OAlc OE
+
+delete_atoms overlap 2.0 H2O PEG mol yes
+
+fix mynpt all npt temp 300 300 100 x 1 1 1000
+timestep 1.0
+
+dump mydmp all image 1000 dump.*.ppn type &
+ type shiny 0.1 box no 0.01 &
+ view 0 90 zoom 1.8  fsaa yes bond atom 0.8 
+dump_modify mydmp backcolor white &
+ acolor OW red acolor HW white &
+ acolor OE red acolor OAlc red &
+ acolor C gray acolor CPos gray &
+ acolor H white acolor HC white &
+ adiam OW 0.2 adiam HW 0.2 &
+ adiam C 3 adiam CPos 3 adiam OAlc 2.8 &
+ adiam H 1 adiam HC 1 adiam OE 2.8
+
+thermo 1000
+
+run 30000
+write_data mix.data

files/tutorial3/pullonPEG/input.lmp

@@ -0,0 +1,59 @@
+variable f0 equal 5
+
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+pair_style lj/cut/coul/long 10
+kspace_style pppm 1e-5
+special_bonds lj 0.0 0.0 0.5 &
+coul 0.0 0.0 1.0 &
+angle yes dihedral yes
+
+read_data ../mergePEGH2O/mix.data
+include ../PARM.lmp
+
+group H2O type OW HW
+group PEG type C CPos H HC OAlc OE
+group ends type OAlc
+variable xcm equal xcm(ends,x)
+variable oxies atom type==label2type(atom,OAlc)
+variable end1 atom v_oxies*(x>v_xcm)
+variable end2 atom v_oxies*(x<v_xcm)
+
+group topull1 variable end1
+group topull2 variable end2
+
+dump mydmp all image 1000 dump.*.ppn type &
+type shiny 0.1 box no 0.01 &
+view 0 90 zoom 1.8 fsaa yes bond atom 0.8
+dump_modify mydmp backcolor white &
+acolor OW red acolor HW white &
+acolor OE red acolor OAlc red &
+acolor C gray acolor CPos gray &
+acolor H white acolor HC white &
+adiam OW 0.2 adiam HW 0.2 &
+adiam C 3 adiam CPos 3 adiam OAlc 2.8 &
+adiam H 1 adiam HC 1 adiam OE 2.8
+
+variable x1 equal xcm(topull1,x)
+variable x2 equal xcm(topull2,x)
+variable y1 equal xcm(topull1,y)
+variable y2 equal xcm(topull2,y)
+variable z1 equal xcm(topull1,z)
+variable z2 equal xcm(topull2,z)
+variable delta_r equal sqrt((v_x1-v_x2)^2+(v_y1-v_y2)^2+(v_z1-v_z2)^2) 
+compute rgyr PEG gyration
+thermo_style custom step temp etotal v_delta_r c_rgyr
+thermo 1000
+
+timestep 1.0
+fix mynvt all nvt temp 300 300 100
+
+run 30000
+
+fix myaf1 topull1 addforce ${f0} 0 0
+fix myaf2 topull2 addforce -${f0} 0 0
+
+run 30000

files/tutorial3/pureH2O/input.lmp

@@ -0,0 +1,49 @@
+
+units real
+atom_style full
+bond_style harmonic
+angle_style harmonic
+dihedral_style harmonic
+pair_style lj/cut/coul/long 10
+kspace_style pppm 1e-5
+special_bonds lj 0.0 0.0 0.5 &
+coul 0.0 0.0 1.0 angle yes
+
+region box block -45 45 -15 15 -15 15
+  create_box 8 box &
+  bond/types 7 &
+  angle/types 8 &
+  dihedral/types 4 &
+  extra/bond/per/atom 3 &
+  extra/angle/per/atom 6 &
+  extra/dihedral/per/atom 10 &
+  extra/special/per/atom 14
+
+include ../PARM.lmp
+
+molecule h2omol H2O-SPCFw.mol
+create_atoms 0 random 1050 87910 NULL mol &
+h2omol 454756 overlap 1.0 maxtry 50
+
+group H2O type OW HW
+minimize 1.0e-4 1.0e-6 100 1000
+reset_timestep 0
+
+fix mynpt all npt temp 300 300 100 &
+  iso 1 1 1000
+
+dump mydmp all image 500 dump.*.jpg type type &
+  shiny 0.1 box no 0.01 view 0 90 zoom 1.8
+dump_modify mydmp backcolor white &
+  acolor OW red acolor HW white &
+  adiam OW 3 adiam HW 1.5
+
+variable myvol equal vol
+variable myoxy equal count(H2O)/3
+variable rho equal ${myoxy}/v_myvol
+thermo 1000
+thermo_style custom step temp etotal v_myvol v_rho
+
+timestep 1.0
+run 20000
+write_data H2O.data