diff --git a/GcmcTutorial/GcmcLj/DoBlockAveraging.sh b/GcmcTutorial/GcmcLj/DoBlockAveraging.sh new file mode 100755 index 0000000..84ff4b6 --- /dev/null +++ b/GcmcTutorial/GcmcLj/DoBlockAveraging.sh @@ -0,0 +1,42 @@ +#! /bin/bash + +MCReportFiles=`find -type f -name MCReport.prod.dat` + +echo "# mu [kJ/mol] Rho [1/(nm^3)] Err Rho [1/(nm^3)]" > rho_of_mu.dat +for MCReportFile in $MCReportFiles +do + grep -v \# $MCReportFile | awk '{print $1,$4}' > Rho.xvg + g_analyze -f Rho.xvg -ee Err.xvg > /dev/null 2>&1 + rm -f \#* + Mu=`echo $MCReportFile | sed -e s/"\/"/\ /g | awk '{print $2}' | sed -e s/mu//` + AvRho=`grep \"av Err.xvg | sed -e s/\"//g | awk '{print $(NF)}'` + SdRho=`grep \"ee Err.xvg | sed -e s/\"//g | awk '{print $(NF)}'` + echo $Mu $AvRho $SdRho +done | sort -n >> rho_of_mu.dat +rm Rho.xvg Err.xvg + +NA="6.0221415e23" +MCReportFile=`echo $MCReportFiles | awk '{print $(NF)}'` +Lambda3=`grep "\# De Broglie Wavelength\^3 \[l\/mol\]" $MCReportFile | awk '{print $(NF-4)}'` #l/mol +DmPerM=10.0 +NmPerM=1.0e9 +Kilo=1000.0 +R=8.314472 #J/mol/K +T=`grep "\# De Broglie Wavelength\^3 \[l\/mol\]" $MCReportFile | awk '{print $(NF-1)}'` #K + +echo "# mu [kJ/mol] Rho [mol/l] Err Rho [mol/l]" > rho_of_mu_in_mol_p_l.dat +grep -v \# rho_of_mu.dat | awk '{f='$NmPerM'^3/'$Kilo'/'$NA';print $1,f*$2,f*$3}' >> rho_of_mu_in_mol_p_l.dat + +echo "# rho [mol/l] sdrho [mol/l] mu [kJ/mol] muid[kJ/mol] muex [kJ/mol] sdmuex [kJ/mol]" > mu_of_rho_in_mol_p_l.dat +grep -v \# rho_of_mu_in_mol_p_l.dat | awk ' +{ +rho=$2; +sdrho=$3; +mu=$1; +muid='$R'*'$T'*log(rho*'$Lambda3')/'$Kilo'; +muex=mu-muid; +sdmuex='$R'*'$T'/rho*sdrho/'$Kilo'; +print rho, sdrho, mu, muid, muex, sdmuex; +}' >> mu_of_rho_in_mol_p_l.dat + +exit diff --git a/GcmcTutorial/GcmcLj/RunEos.sh b/GcmcTutorial/GcmcLj/RunEos.sh new file mode 100755 index 0000000..d17c206 --- /dev/null +++ b/GcmcTutorial/GcmcLj/RunEos.sh @@ -0,0 +1,29 @@ +#! /bin/bash + +GMXINSTALLDIR="../../gromacs/gromacs-4.0.7/gromacs-4.0.7-git/install/" +source ../SourceGromPyEnv.sh + +InputParFile="start.dat" +MuList=`grep -v \# $InputParFile | awk '{print $3}' | sort -n` +TprDir=$PWD"/tpr" +PyLogFile="py.log" +NMin=0 +NMax=426 +GCMCMol="W" +GcmcPy=testHybrid.py + +for i in $MuList +do + Mu=$i + NStart=`grep "mu"$i $InputParFile| awk '{print $2}'` + echo "Performing MuVT simulation @ Mu=$Mu ..." + cd "mu$i" + time ../../../$GcmcPy $TprDir $Mu $NStart $GCMCMol $NMin $NMax 2> /dev/null > $PyLogFile + rm -f \#* + gzip -f md.log + gzip -f py.log + echo + cd ../ +done + +exit diff --git a/GcmcTutorial/GcmcLj/gro/GenerateStartingStructures.sh b/GcmcTutorial/GcmcLj/gro/GenerateStartingStructures.sh new file mode 100755 index 0000000..95be3d6 --- /dev/null +++ b/GcmcTutorial/GcmcLj/gro/GenerateStartingStructures.sh @@ -0,0 +1,44 @@ +#! /bin/bash + +EXPECTED_N_ARGS=3 +if [ $# -ne $EXPECTED_N_ARGS ]; then + echo "Input the correct amount of arguments!" + echo "Usage:" + echo "------" + echo "./GenerateStartingStructures.sh \"StartOfNRange\" \"EndOfNRange\" \"WInputN.gro\"" + echo "Example: ./GenerateStartingStructures.sh 1 430 W400.gro" + echo "EXITING..." + exit 1 +fi + +NStart=$1 +NEnd=$2 +NInputFile=$3 +NInput=`echo $NInputFile | cut -d. -f1 | sed -e s/W//` + +declare -i N=$NStart +while [ $N -lt $NInput ] +do + head -1 $NInputFile > tmp.gro + echo $N >> tmp.gro + head -$(($N+2)) $NInputFile | tail -$N >> tmp.gro + tail -1 $NInputFile >> tmp.gro + mv tmp.gro W$N.gro + N=$N+1 +done +declare -i N=$(($NInput+1)) +while [ $N -le $NEnd ] +do + PrevN=$(($N-1)) + head -1 $NInputFile > tmp.gro + echo $N >> tmp.gro + head -$(($PrevN+2)) W$PrevN.gro | tail -$PrevN >> tmp.gro + tail -2 W$PrevN.gro | head -1 | sed -e s/"$PrevN"W/"$N"W/ >> tmp.gro + tail -1 $NInputFile >> tmp.gro + editconf -f tmp.gro -o W$N.gro + rm -f tmp.gro + rm -f \#* + N=$N+1 +done + +exit diff --git a/GcmcTutorial/GcmcLj/initstructure/water.gro b/GcmcTutorial/GcmcLj/initstructure/water.gro new file mode 100644 index 0000000..147f568 --- /dev/null +++ b/GcmcTutorial/GcmcLj/initstructure/water.gro @@ -0,0 +1,403 @@ +WATER + 400 + 1W W 1 0.084 3.595 3.359 0.0663 0.0148 0.2032 + 2W W 2 0.460 2.488 2.882 0.0999 -0.0648 -0.1661 + 3W W 3 3.165 2.218 0.652 -0.0881 -0.1237 -0.0896 + 4W W 4 3.295 3.303 2.679 -0.1486 -0.3229 0.1120 + 5W W 5 1.213 3.294 0.205 -0.1053 -0.1062 0.1014 + 6W W 6 1.296 1.446 1.188 0.0877 -0.0566 -0.1282 + 7W W 7 0.811 1.294 1.352 0.1967 0.2199 0.3289 + 8W W 8 1.802 2.109 0.786 -0.1596 -0.1576 -0.0010 + 9W W 9 1.477 3.201 3.141 -0.1225 0.0135 0.1267 + 10W W 10 0.126 0.762 3.104 0.0776 -0.1781 -0.1549 + 11W W 11 0.888 0.042 2.906 0.1622 -0.2895 -0.1539 + 12W W 12 2.582 0.430 1.793 0.0293 0.1399 0.1850 + 13W W 13 2.231 1.301 0.363 0.0119 0.0262 -0.0578 + 14W W 14 2.801 0.735 3.454 0.2122 -0.0713 -0.1525 + 15W W 15 0.167 0.527 2.579 -0.2237 -0.0155 -0.0333 + 16W W 16 0.266 3.146 3.600 0.0972 -0.2452 0.1849 + 17W W 17 1.788 2.536 0.332 0.0552 0.0717 0.1324 + 18W W 18 0.220 1.319 2.025 0.1433 0.0166 -0.2722 + 19W W 19 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2.109 -0.0167 -0.0406 -0.0423 + 396W W 396 1.639 1.110 3.319 0.0300 -0.3053 0.0710 + 397W W 397 2.090 3.276 0.830 -0.0307 0.0044 0.1215 + 398W W 398 1.398 2.531 3.468 0.0631 -0.0196 -0.4235 + 399W W 399 1.524 2.769 0.845 -0.5337 0.0559 0.0075 + 400W W 400 0.745 1.509 0.104 0.1616 -0.0161 0.1005 + 3.64428 3.64428 3.64428 diff --git a/GcmcTutorial/GcmcLj/itp/martini_v2.1.itp b/GcmcTutorial/GcmcLj/itp/martini_v2.1.itp new file mode 100644 index 0000000..16ab725 --- /dev/null +++ b/GcmcTutorial/GcmcLj/itp/martini_v2.1.itp @@ -0,0 +1,594 @@ +; MARTINI FORCEFIELD V2.0 +; +; SJ MARRINK, 01-07-2007 +; +; please cite: +; +; S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H. de Vries. +; The MARTINI forcefield: coarse grained model for biomolecular simulations. +; JPC-B, 111:7812-7824, 2007. +; +; and (if using lipid topologies): +; +; S.J. Marrink, A.H. de Vries, A.E. Mark. +; Coarse grained model for semi-quantitative lipid simulations. +; JPC-B, 108:750-760, 2004. + + +[ defaults ] +1 1 + +[ atomtypes ] + +; Currently eighteen particle types are defined, divided into four main categories +; (P, polar; N, intermediate; C, apolar; Q, charged) +; each of which has a number of sublevels (0,a,d, or ad) +; subtype 0 has no hydrogen bond forming capacities, +; subtype d has some hydrogen donor capacities, +; subtype a some hydrogen acceptor capacities, +; and subtype da has both donor and acceptor capacities +; or (1,2,3,4,5) where subtype 5 is more polar than 1. + +; Two main classes of particles are furthermore distinguished, namely +; STANDARD particles which are mapped using a 4:1 mapping scheme, and +; RING particles which are used for ring compounds mapped 2-3:1. +; A special BIG particle type is defined in addition to prevent freezing of CG water. + +; For reasons of computational efficiency, all particle masses are set to 72 amu. +; For realistic dynamics, especially of ring systems, the particle masses should be adapted. +; This might require a reduction of the integration timestep, however. + +; name mass charge ptype c6 c12 + +; STANDARD types, 4:1 mapping +; polar type +P5 72.0 0.000 A 0.0 0.0 +P4 72.0 0.000 A 0.0 0.0 +P3 72.0 0.000 A 0.0 0.0 +P2 72.0 0.000 A 0.0 0.0 +P1 72.0 0.000 A 0.0 0.0 +; intermediate polar +Nda 72.0 0.000 A 0.0 0.0 +Nd 72.0 0.000 A 0.0 0.0 +Na 72.0 0.000 A 0.0 0.0 +N0 72.0 0.000 A 0.0 0.0 +; apolar +C5 72.0 0.000 A 0.0 0.0 +C4 72.0 0.000 A 0.0 0.0 +C3 72.0 0.000 A 0.0 0.0 +C2 72.0 0.000 A 0.0 0.0 +C1 72.0 0.000 A 0.0 0.0 +; charged +Qda 72.0 0.000 A 0.0 0.0 +Qd 72.0 0.000 A 0.0 0.0 +Qa 72.0 0.000 A 0.0 0.0 +Q0 72.0 0.000 A 0.0 0.0 + +; RING types, 2-3:1 mapping (only few types are defined here) +SP4 72.0 0.000 A 0.0 0.0 +SP1 72.0 0.000 A 0.0 0.0 +SNd 72.0 0.000 A 0.0 0.0 +SNa 72.0 0.000 A 0.0 0.0 +SC5 72.0 0.000 A 0.0 0.0 +SC4 72.0 0.000 A 0.0 0.0 +SC3 72.0 0.000 A 0.0 0.0 +SC2 72.0 0.000 A 0.0 0.0 +SC1 72.0 0.000 A 0.0 0.0 + +; AMINO ACIDS (required for Q-C interactions inside proteins) +AC2 72.0 0.000 A 0.0 0.0 +AC1 72.0 0.000 A 0.0 0.0 + +; BIG particle type (to prevent freezing of water) +BP4 72.0 0.000 A 0.0 0.0 + + +[ nonbond_params ] + +; levels of LJ interaction: + +; O - supra attractive: (eps=5.6, s=0.47) +; I - attractive: (eps=5.0, s=0.47) +; II - almost attractive: (eps=4.5, s=0.47) +; III - semi attractive: (eps=4.0, s=0.47) +; IV - intermediate: (eps=3.5, s=0.47) +; V - almost intermediate: (eps=3.1, s=0.47) +; VI - semi repulsive: (eps=2.7, s=0.47) +; VII - almost repulsive: (eps=2.3, s=0.47) +; VIII - repulsive: (eps=2.0, s=0.47) +; IX - super repulsive: (eps=2.0, s=0.62) +; +; RINGS: for ring-ring interactions eps is reduced to 75%, sigma=0.43. + +; i j funda c6 c12 +; self terms + P5 P5 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 P4 1 0.21558E-00 0.23238E-02 ; attractive + BP4 BP4 1 0.21558E-00 0.23238E-02 ; attractive + SP4 SP4 1 0.94820E-01 0.59939E-03 ; 75attractive, s=0.43 + P3 P3 1 0.21558E-00 0.23238E-02 ; attractive + P2 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SP1 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + Nda Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + Nd Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd SNd 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + Na Na 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa SNa 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + N0 N0 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SC5 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C4 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SC4 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C3 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C2 C2 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + SC2 SC2 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + C1 C1 1 0.15091E-00 0.16267E-02 ; intermediate + AC1 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + SC1 SC1 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + Qda Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + Qd Qd 1 0.21558E-00 0.23238E-02 ; attractive + Qa Qa 1 0.21558E-00 0.23238E-02 ; attractive + Q0 Q0 1 0.15091E-00 0.16267E-02 ; intermediate +; cross terms + P5 P4 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 BP4 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SP4 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P3 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P2 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 P1 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 SP1 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Nda 1 0.21558E-00 0.23238E-02 ; attractive + P5 Nd 1 0.21558E-00 0.23238E-02 ; attractive + P5 SNd 1 0.21558E-00 0.23238E-02 ; attractive + P5 Na 1 0.21558E-00 0.23238E-02 ; attractive + P5 SNa 1 0.21558E-00 0.23238E-02 ; attractive + P5 N0 1 0.15091E-00 0.16267E-02 ; intermediate + P5 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P5 SC5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P5 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 SC4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P5 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P5 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P5 SC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P5 C1 1 0.86233E-01 0.92953E-03 ; repulsive + P5 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + P5 SC1 1 0.86233E-01 0.92953E-03 ; repulsive + P5 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + P5 Q0 1 0.21558E-00 0.23238E-02 ; attractive + P4 BP4 1 0.76824E-00 0.26348E-01 ; supra attractive, s=0.57 + P4 SP4 1 0.21558E-00 0.23238E-02 ; attractive + P4 P3 1 0.21558E-00 0.23238E-02 ; attractive + P4 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P4 Nda 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 SNd 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 Na 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 SNa 1 0.17246E-00 0.18590E-02 ; semi attractive + P4 N0 1 0.15091E-00 0.16267E-02 ; intermediate + P4 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P4 SC5 1 0.13366E-00 0.14408E-02 ; almost intermediate + P4 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 SC4 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + P4 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P4 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P4 SC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + P4 C1 1 0.86233E-01 0.92953E-03 ; repulsive + P4 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + P4 SC1 1 0.86233E-01 0.92953E-03 ; repulsive + P4 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + P4 Q0 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 SP4 1 0.21558E-00 0.23238E-02 ; attractive + BP4 P3 1 0.21558E-00 0.23238E-02 ; attractive + BP4 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + BP4 Nda 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 SNd 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 Na 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 SNa 1 0.17246E-00 0.18590E-02 ; semi attractive + BP4 N0 1 0.15091E-00 0.16267E-02 ; intermediate + BP4 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + BP4 SC5 1 0.13366E-00 0.14408E-02 ; almost intermediate + BP4 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 SC4 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + BP4 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + BP4 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + BP4 SC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + BP4 C1 1 0.86233E-01 0.92953E-03 ; repulsive + BP4 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + BP4 SC1 1 0.86233E-01 0.92953E-03 ; repulsive + BP4 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + BP4 Q0 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 P3 1 0.21558E-00 0.23238E-02 ; attractive + SP4 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + SP4 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + SP4 SP1 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP4 Nda 1 0.17246E-00 0.18590E-02 ; semi attractive + SP4 Nd 1 0.17246E-00 0.18590E-02 ; semi attractive + SP4 SNd 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP4 Na 1 0.17246E-00 0.18590E-02 ; semi attractive + SP4 SNa 1 0.75856E-01 0.47952E-03 ; 75semi attractive, s=0.43 + SP4 N0 1 0.15091E-00 0.16267E-02 ; intermediate + SP4 C5 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP4 SC5 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP4 C4 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP4 SC4 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP4 C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP4 SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP4 C2 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP4 AC2 1 0.99167E-01 0.10690E-02 ; almost repulsive + SP4 SC2 1 0.43617E-01 0.27572E-03 ; 75almost repulsive, s=0.43 + SP4 C1 1 0.86233E-01 0.92953E-03 ; repulsive + SP4 AC1 1 0.86233E-01 0.92953E-03 ; repulsive + SP4 SC1 1 0.37928E-01 0.23976E-03 ; 75repulsive, s=0.43 + SP4 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + SP4 Q0 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 P2 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + P3 N0 1 0.15091E-00 0.16267E-02 ; intermediate + P3 C5 1 0.15091E-00 0.16267E-02 ; intermediate + P3 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + P3 C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 C3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 SC3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P3 C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P3 AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P3 SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P3 C1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P3 AC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P3 SC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P3 Qda 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + P3 Q0 1 0.21558E-00 0.23238E-02 ; attractive + P2 P1 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + P2 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + P2 C5 1 0.15091E-00 0.16267E-02 ; intermediate + P2 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + P2 C4 1 0.15091E-00 0.16267E-02 ; intermediate + P2 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + P2 C3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P2 SC3 1 0.13366E-00 0.14408E-02 ; almost intermediate + P2 C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P2 AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P2 SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + P2 C1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P2 AC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P2 SC1 1 0.99167E-01 0.10690E-02 ; almost repulsive + P2 Qda 1 0.21558E-00 0.23238E-02 ; attractive + P2 Qd 1 0.21558E-00 0.23238E-02 ; attractive + P2 Qa 1 0.21558E-00 0.23238E-02 ; attractive + P2 Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 SP1 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + P1 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + P1 C5 1 0.15091E-00 0.16267E-02 ; intermediate + P1 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + P1 C4 1 0.15091E-00 0.16267E-02 ; intermediate + P1 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + P1 C3 1 0.15091E-00 0.16267E-02 ; intermediate + P1 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + P1 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + P1 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + P1 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + P1 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + P1 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + P1 SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + P1 Qda 1 0.21558E-00 0.23238E-02 ; attractive + P1 Qd 1 0.21558E-00 0.23238E-02 ; attractive + P1 Qa 1 0.21558E-00 0.23238E-02 ; attractive + P1 Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SP1 Nda 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SNd 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP1 Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SP1 SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SP1 N0 1 0.17246E-00 0.18590E-02 ; semi attractive + SP1 C5 1 0.15091E-00 0.16267E-02 ; intermediate + SP1 SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP1 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SP1 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP1 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SP1 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SP1 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP1 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SP1 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SP1 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP1 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SP1 SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SP1 Qda 1 0.21558E-00 0.23238E-02 ; attractive + SP1 Qd 1 0.21558E-00 0.23238E-02 ; attractive + SP1 Qa 1 0.21558E-00 0.23238E-02 ; attractive + SP1 Q0 1 0.21558E-00 0.23238E-02 ; attractive + Nda Nd 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda SNd 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda Na 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + Nda N0 1 0.15091E-00 0.16267E-02 ; intermediate + Nda C5 1 0.15091E-00 0.16267E-02 ; intermediate + Nda SC5 1 0.15091E-00 0.16267E-02 ; intermediate + Nda C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nda SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nda C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nda Qda 1 0.21558E-00 0.23238E-02 ; attractive + Nda Qd 1 0.21558E-00 0.23238E-02 ; attractive + Nda Qa 1 0.21558E-00 0.23238E-02 ; attractive + Nda Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd SNd 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd Na 1 0.19402E-00 0.20914E-02 ; almost attractive + Nd SNa 1 0.19402E-00 0.20914E-02 ; almost attractive + Nd N0 1 0.15091E-00 0.16267E-02 ; intermediate + Nd C5 1 0.15091E-00 0.16267E-02 ; intermediate + Nd SC5 1 0.15091E-00 0.16267E-02 ; intermediate + Nd C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nd SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Nd C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Nd Qda 1 0.21558E-00 0.23238E-02 ; attractive + Nd Qd 1 0.17246E-00 0.18590E-02 ; semi attractive + Nd Qa 1 0.21558E-00 0.23238E-02 ; attractive + Nd Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd Na 1 0.19402E-00 0.20914E-02 ; almost attractive + SNd SNa 1 0.85338E-01 0.53946E-03 ; 75almost attractive, s=0.43 + SNd N0 1 0.15091E-00 0.16267E-02 ; intermediate + SNd C5 1 0.15091E-00 0.16267E-02 ; intermediate + SNd SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNd C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + SNd SC4 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SNd C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNd C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNd C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNd SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNd Qda 1 0.21558E-00 0.23238E-02 ; attractive + SNd Qd 1 0.17246E-00 0.18590E-02 ; semi attractive + SNd Qa 1 0.21558E-00 0.23238E-02 ; attractive + SNd Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + Na SNa 1 0.17246E-00 0.18590E-02 ; semi attractive + Na N0 1 0.15091E-00 0.16267E-02 ; intermediate + Na C5 1 0.15091E-00 0.16267E-02 ; intermediate + Na SC5 1 0.15091E-00 0.16267E-02 ; intermediate + Na C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Na SC4 1 0.13366E-00 0.14408E-02 ; almost intermediate + Na C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na SC3 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na SC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + Na Qda 1 0.21558E-00 0.23238E-02 ; attractive + Na Qd 1 0.21558E-00 0.23238E-02 ; attractive + Na Qa 1 0.17246E-00 0.18590E-02 ; semi attractive + Na Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa N0 1 0.15091E-00 0.16267E-02 ; intermediate + SNa C5 1 0.15091E-00 0.16267E-02 ; intermediate + SNa SC5 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SNa C4 1 0.13366E-00 0.14408E-02 ; almost intermediate + SNa SC4 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SNa C3 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa SC3 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNa C2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa AC2 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa SC2 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNa C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + SNa SC1 1 0.51203E-01 0.32367E-03 ; 75semi repulsive s=0.43 + SNa Qda 1 0.21558E-00 0.23238E-02 ; attractive + SNa Qd 1 0.17246E-00 0.18590E-02 ; semi attractive + SNa Qa 1 0.21558E-00 0.23238E-02 ; attractive + SNa Q0 1 0.17246E-00 0.18590E-02 ; semi attractive + N0 C5 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C4 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C3 1 0.15091E-00 0.16267E-02 ; intermediate + N0 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + N0 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + N0 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + N0 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + N0 C1 1 0.11642E-00 0.12549E-02 ; semi repulsive + N0 AC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + N0 SC1 1 0.11642E-00 0.12549E-02 ; semi repulsive + N0 Qda 1 0.15091E-00 0.16267E-02 ; intermediate + N0 Qd 1 0.15091E-00 0.16267E-02 ; intermediate + N0 Qa 1 0.15091E-00 0.16267E-02 ; intermediate + N0 Q0 1 0.15091E-00 0.16267E-02 ; intermediate + C5 SC5 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C4 1 0.15091E-00 0.16267E-02 ; intermediate + C5 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C3 1 0.15091E-00 0.16267E-02 ; intermediate + C5 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + C5 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 SC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Qda 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Qd 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Qa 1 0.13366E-00 0.14408E-02 ; almost intermediate + C5 Q0 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 C4 1 0.15091E-00 0.16267E-02 ; intermediate + SC5 SC4 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC5 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SC5 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC5 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 SC1 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC5 Qda 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 Qd 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 Qa 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC5 Q0 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 SC4 1 0.15091E-00 0.16267E-02 ; intermediate + C4 C3 1 0.15091E-00 0.16267E-02 ; intermediate + C4 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + C4 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 SC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 SC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + C4 Qda 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 Qd 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 Qa 1 0.11642E-00 0.12549E-02 ; semi repulsive + C4 Q0 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 C3 1 0.15091E-00 0.16267E-02 ; intermediate + SC4 SC3 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC4 C2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 AC2 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 SC2 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC4 C1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 AC1 1 0.13366E-00 0.14408E-02 ; almost intermediate + SC4 SC1 1 0.58789E-01 0.37162E-03 ; 75almost intermediate, s=0.43 + SC4 Qda 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 Qd 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 Qa 1 0.11642E-00 0.12549E-02 ; semi repulsive + SC4 Q0 1 0.11642E-00 0.12549E-02 ; semi repulsive + C3 SC3 1 0.15091E-00 0.16267E-02 ; intermediate + C3 C2 1 0.15091E-00 0.16267E-02 ; intermediate + C3 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + C3 SC2 1 0.15091E-00 0.16267E-02 ; intermediate + C3 C1 1 0.15091E-00 0.16267E-02 ; intermediate + C3 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + C3 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + C3 Qda 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 Qd 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 Qa 1 0.99167E-01 0.10690E-02 ; almost repulsive + C3 Q0 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 C2 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 SC2 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC3 C1 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + SC3 SC1 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC3 Qda 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 Qd 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 Qa 1 0.99167E-01 0.10690E-02 ; almost repulsive + SC3 Q0 1 0.99167E-01 0.10690E-02 ; almost repulsive + C2 AC2 1 0.15091E-00 0.16267E-02 ; intermediate + C2 SC2 1 0.15091E-00 0.16267E-02 ; intermediate + C2 C1 1 0.15091E-00 0.16267E-02 ; intermediate + C2 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + C2 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + C2 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C2 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + AC2 SC2 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 C1 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + AC2 Qda 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 Qd 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 Qa 1 0.86233E-01 0.92953E-03 ; repulsive + AC2 Q0 1 0.86233E-01 0.92953E-03 ; repulsive + SC2 C1 1 0.15091E-00 0.16267E-02 ; intermediate + SC2 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + SC2 SC1 1 0.66375E-01 0.41957E-03 ; 75intermediate, s=0.43 + SC2 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC2 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 AC1 1 0.15091E-00 0.16267E-02 ; intermediate + C1 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + C1 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + C1 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + AC1 SC1 1 0.15091E-00 0.16267E-02 ; intermediate + AC1 Qda 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 Qd 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 Qa 1 0.86233E-01 0.92953E-03 ; repulsive + AC1 Q0 1 0.86233E-01 0.92953E-03 ; repulsive + SC1 Qda 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 Qd 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 Qa 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + SC1 Q0 1 0.45440E-00 0.25810E-01 ; super repulsive, s=0.62 + Qda Qd 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + Qda Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + Qd Qa 1 0.24145E-00 0.26027E-02 ; supra attractive + Qd Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + Qa Q0 1 0.19402E-00 0.20914E-02 ; almost attractive + + + +;;;;;; WATER (representing 4 H2O molecules) + +[ moleculetype ] +; molname nrexcl + W 1 + +[ atoms ] +;id type resnr residu atom cgnr charge + 1 P4 1 W W 1 0 + +;;;;;; ANTIFREEZE (prevents freezing of water) + +[ moleculetype ] +; molname nrexcl + WF 1 + +[ atoms ] +;id type resnr residu atom cgnr charge + 1 BP4 1 WF WF 1 0 + + diff --git a/GcmcTutorial/GcmcLj/mdp/gcmc.mdp b/GcmcTutorial/GcmcLj/mdp/gcmc.mdp new file mode 100644 index 0000000..db2bb6f --- /dev/null +++ b/GcmcTutorial/GcmcLj/mdp/gcmc.mdp @@ -0,0 +1,300 @@ +; +; File 'mdout.mdp' was generated +; By user: rpool (1000) +; On host: rini +; At date: Mon Nov 29 14:18:04 2010 +; + +; VARIOUS PREPROCESSING OPTIONS +; Preprocessor information: use cpp syntax. +; e.g.: -I/home/joe/doe -I/home/mary/hoe +include = +; e.g.: -DI_Want_Cookies -DMe_Too +define = + +; RUN CONTROL PARAMETERS +integrator = md +; Start time and timestep in ps +tinit = 0.0 +dt = 0.02 +nsteps = 100 +; For exact run continuation or redoing part of a run +; Part index is updated automatically on checkpointing (keeps files separate) +simulation_part = 1 +init_step = 0 +; mode for center of mass motion removal +comm-mode = Linear +; number of steps for center of mass motion removal +nstcomm = 1 +; group(s) for center of mass motion removal +comm_grps = System + +; LANGEVIN DYNAMICS OPTIONS +; Friction coefficient (amu/ps) and random seed +bd-fric = 0 +ld-seed = 1993 + +; ENERGY MINIMIZATION OPTIONS +; Force tolerance and initial step-size +emtol = 10 +emstep = 0.01 +; Max number of iterations in relax_shells +niter = 20 +; Step size (ps^2) for minimization of flexible constraints +fcstep = 0 +; Frequency of steepest descents steps when doing CG +nstcgsteep = 1000 +nbfgscorr = 10 + +; TEST PARTICLE INSERTION OPTIONS +rtpi = 0.05 + +; OUTPUT CONTROL OPTIONS +; Output frequency for coords (x), velocities (v) and forces (f) +nstxout = 100 +nstvout = 100 +nstfout = 100 +; Output frequency for energies to log file and energy file +nstlog = 0 +nstenergy = 100 +; Output frequency and precision for xtc file +nstxtcout = 100 +xtc_precision = 1000 +; This selects the subset of atoms for the xtc file. You can +; select multiple groups. By default all atoms will be written. +xtc-grps = +; Selection of energy groups +energygrps = W + +; NEIGHBORSEARCHING PARAMETERS +; nblist update frequency +nstlist = 10 +; ns algorithm (simple or grid) +ns-type = Grid +; Periodic boundary conditions: xyz, no, xy +pbc = xyz +periodic_molecules = no +; nblist cut-off +rlist = 1.2 + +; OPTIONS FOR ELECTROSTATICS AND VDW +; Method for doing electrostatics +coulombtype = shift +rcoulomb-switch = 0 +rcoulomb = 1.2 +; Relative dielectric constant for the medium and the reaction field +epsilon_r = 15 +epsilon_rf = 1 +; Method for doing Van der Waals +vdw_type = shift +; cut-off lengths +rvdw_switch = 0.9 +rvdw = 1.2 +; Apply long range dispersion corrections for Energy and Pressure +DispCorr = No +; Extension of the potential lookup tables beyond the cut-off +table-extension = 1 +; Seperate tables between energy group pairs +energygrp_table = +; Spacing for the PME/PPPM FFT grid +fourierspacing = 0.12 +; FFT grid size, when a value is 0 fourierspacing will be used +fourier_nx = 10 +fourier_ny = 10 +fourier_nz = 10 +; EWALD/PME/PPPM parameters +pme_order = 4 +ewald_rtol = 1e-05 +ewald_geometry = 3d +epsilon_surface = 0 +optimize_fft = no + +; IMPLICIT SOLVENT ALGORITHM +implicit_solvent = No + +; GENERALIZED BORN ELECTROSTATICS +; Algorithm for calculating Born radii +gb_algorithm = Still +; Frequency of calculating the Born radii inside rlist +nstgbradii = 1 +; Cutoff for Born radii calculation; the contribution from atoms +; between rlist and rgbradii is updated every nstlist steps +rgbradii = 2 +; Dielectric coefficient of the implicit solvent +gb_epsilon_solvent = 80 +; Salt concentration in M for Generalized Born models +gb_saltconc = 0 +; Scaling factors used in the OBC GB model. Default values are OBC(II) +gb_obc_alpha = 1 +gb_obc_beta = 0.8 +gb_obc_gamma = 4.85 +; Surface tension (kJ/mol/nm^2) for the SA (nonpolar surface) part of GBSA +; The default value (2.092) corresponds to 0.005 kcal/mol/Angstrom^2. +sa_surface_tension = 2.092 + +; OPTIONS FOR WEAK COUPLING ALGORITHMS +; Temperature coupling +tcoupl = Berendsen +; Groups to couple separately +tc-grps = System +; Time constant (ps) and reference temperature (K) +tau_t = 0.1 +ref_t = 773 +; Pressure coupling +Pcoupl = no +Pcoupltype = isotropic +; Time constant (ps), compressibility (1/bar) and reference P (bar) +tau_p = 0.5 +compressibility = 1e-5 +ref_p = 1.0 +; Scaling of reference coordinates, No, All or COM +refcoord_scaling = No +; Random seed for Andersen thermostat +andersen_seed = 815131 + +; OPTIONS FOR QMMM calculations +QMMM = no +; Groups treated Quantum Mechanically +QMMM-grps = +; QM method +QMmethod = +; QMMM scheme +QMMMscheme = normal +; QM basisset +QMbasis = +; QM charge +QMcharge = +; QM multiplicity +QMmult = +; Surface Hopping +SH = +; CAS space options +CASorbitals = +CASelectrons = +SAon = +SAoff = +SAsteps = +; Scale factor for MM charges +MMChargeScaleFactor = 1 +; Optimization of QM subsystem +bOPT = +bTS = + +; SIMULATED ANNEALING +; Type of annealing for each temperature group (no/single/periodic) +annealing = +; Number of time points to use for specifying annealing in each group +annealing_npoints = +; List of times at the annealing points for each group +annealing_time = +; Temp. at each annealing point, for each group. +annealing_temp = + +; GENERATE VELOCITIES FOR STARTUP RUN +gen-vel = no +gen-temp = 773 +gen-seed = 173529 + +; OPTIONS FOR BONDS +constraints = none +; Type of constraint algorithm +constraint-algorithm = Lincs +; Do not constrain the start configuration +continuation = no +; Use successive overrelaxation to reduce the number of shake iterations +Shake-SOR = no +; Relative tolerance of shake +shake-tol = 0.0001 +; Highest order in the expansion of the constraint coupling matrix +lincs-order = 4 +; Number of iterations in the final step of LINCS. 1 is fine for +; normal simulations, but use 2 to conserve energy in NVE runs. +; For energy minimization with constraints it should be 4 to 8. +lincs-iter = 1 +; Lincs will write a warning to the stderr if in one step a bond +; rotates over more degrees than +lincs-warnangle = 30 +; Convert harmonic bonds to morse potentials +morse = no + +; ENERGY GROUP EXCLUSIONS +; Pairs of energy groups for which all non-bonded interactions are excluded +energygrp_excl = + +; WALLS +; Number of walls, type, atom types, densities and box-z scale factor for Ewald +nwall = 0 +wall_type = 9-3 +wall_r_linpot = -1 +wall_atomtype = +wall_density = +wall_ewald_zfac = 3 + +; COM PULLING +; Pull type: no, umbrella, constraint or constant_force +pull = no + +; NMR refinement stuff +; Distance restraints type: No, Simple or Ensemble +disre = No +; Force weighting of pairs in one distance restraint: Conservative or Equal +disre-weighting = Conservative +; Use sqrt of the time averaged times the instantaneous violation +disre-mixed = no +disre-fc = 1000 +disre-tau = 0 +; Output frequency for pair distances to energy file +nstdisreout = 100 +; Orientation restraints: No or Yes +orire = no +; Orientation restraints force constant and tau for time averaging +orire-fc = 0 +orire-tau = 0 +orire-fitgrp = +; Output frequency for trace(SD) and S to energy file +nstorireout = 100 +; Dihedral angle restraints: No or Yes +dihre = no +dihre-fc = 1000 + +; Free energy control stuff +free-energy = no +init-lambda = 0 +delta-lambda = 0 +sc-alpha = 0 +sc-power = 0 +sc-sigma = 0.3 +couple-moltype = +couple-lambda0 = vdw-q +couple-lambda1 = vdw-q +couple-intramol = no + +; Non-equilibrium MD stuff +acc-grps = +accelerate = +freezegrps = +freezedim = +cos-acceleration = 0 +deform = + +; Electric fields +; Format is number of terms (int) and for all terms an amplitude (real) +; and a phase angle (real) +E-x = +E-xt = +E-y = +E-yt = +E-z = +E-zt = + +; User defined thingies +user1-grps = +user2-grps = +userint1 = 0 +userint2 = 0 +userint3 = 0 +userint4 = 0 +userreal1 = 0 +userreal2 = 0 +userreal3 = 0 +userreal4 = 0 diff --git a/GcmcTutorial/GcmcLj/mdp/mdeq.mdp b/GcmcTutorial/GcmcLj/mdp/mdeq.mdp new file mode 100644 index 0000000..598fec8 --- /dev/null +++ b/GcmcTutorial/GcmcLj/mdp/mdeq.mdp @@ -0,0 +1,61 @@ +; +; md.mdp +; Generated automatically by: /home/rpool/workspace/PyWork/trunk/Pull/src/MDP.pyc +; User: rpool +; Date: 2010-04-12 +; Time: 16:03:19.797442 +; + +; Preprocessing options: +cpp = /lib/cpp +title = md + +; Run control parameters: +comm_grps = System +integrator = md +dt = 0.002 +nstcomm = 1 +nsteps = 10000 +tinit = 0.0 + +; Output control options: +nstfout = 100 +nstenergy = 100 +nstxtcout = 100 +energygrps = System +xtc_precision = 1000 +nstxout = 100 +nstvout = 100 +nstlog = 100 + +; Neighborsearching parameters: +rlist = 1.2 + +; Options for electrostatics and vdw: +vdw_type = shift +coulombtype = shift +epsilon_r = 15 +fourier_nz = 10 +rcoulomb = 1.2 +fourier_nx = 10 +rvdw_switch = 0.9 +fourier_ny = 10 +rvdw = 1.2 + +; Options for weak coupling algorithms: +tcoupl = Berendsen +tc-grps = System +Pcoupltype = isotropic +ref_p = 20000.0 +Pcoupl = no +ref_t = 773 +andersen_seed = 815131 +compressibility = 1e-5 +tau_t = 0.1 +tau_p = 0.5 + +; Generate velocities for startup run: +gen_vel = yes +gen_temp = 773 +gen_seed = 171533 + diff --git a/GcmcTutorial/GcmcLj/mdp/mdprod.mdp b/GcmcTutorial/GcmcLj/mdp/mdprod.mdp new file mode 100644 index 0000000..5c0bd2f --- /dev/null +++ b/GcmcTutorial/GcmcLj/mdp/mdprod.mdp @@ -0,0 +1,61 @@ +; +; md.mdp +; Generated automatically by: /home/rpool/workspace/PyWork/trunk/Pull/src/MDP.pyc +; User: rpool +; Date: 2010-04-12 +; Time: 16:03:19.797442 +; + +; Preprocessing options: +cpp = /lib/cpp +title = md + +; Run control parameters: +comm_grps = System +integrator = md +dt = 0.02 +nstcomm = 1 +nsteps = 10000 +tinit = 0.0 + +; Output control options: +nstfout = 100 +nstenergy = 100 +nstxtcout = 100 +energygrps = System +xtc_precision = 1000 +nstxout = 100 +nstvout = 100 +nstlog = 100 + +; Neighborsearching parameters: +rlist = 1.2 + +; Options for electrostatics and vdw: +vdw_type = shift +coulombtype = shift +epsilon_r = 15 +fourier_nz = 10 +rcoulomb = 1.2 +fourier_nx = 10 +rvdw_switch = 0.9 +fourier_ny = 10 +rvdw = 1.2 + +; Options for weak coupling algorithms: +tcoupl = Berendsen +tc-grps = System +Pcoupltype = isotropic +ref_p = 20000.0 +Pcoupl = no +ref_t = 773 +andersen_seed = 815131 +compressibility = 1e-5 +tau_t = 0.1 +tau_p = 0.5 + +; Generate velocities for startup run: +gen_vel = yes +gen_temp = 773 +gen_seed = 171533 + diff --git a/GcmcTutorial/GcmcLj/start.dat b/GcmcTutorial/GcmcLj/start.dat new file mode 100644 index 0000000..7e92a68 --- /dev/null +++ b/GcmcTutorial/GcmcLj/start.dat @@ -0,0 +1,30 @@ +mu-156/ 2 -156 +mu-151/ 3 -151 +mu-146/ 7 -146 +mu-140/ 15 -140 +mu-135/ 33 -135 +mu-131/ 60 -131 +mu-129/ 75 -129 +mu-127/ 106 -127 +mu-126/ 142 -126 +mu-125/ 161 -125 +mu-124/ 170 -124 +mu-123/ 209 -123 +mu-122/ 198 -122 +mu-120/ 236 -120 +mu-118/ 259 -118 +mu-115/ 301 -115 +mu-112/ 317 -112 +mu-110/ 100 -110 +mu-108/ 328 -108 +mu-105 195 -105 +mu-102/ 251 -102 +mu-98/ 280 -98 +mu-95/ 303 -95 +mu-91/ 330 -91 +mu-88/ 340 -88 +mu-80/ 370 -80 +mu-79/ 380 -79 +mu-78/ 390 -78 +mu-75/ 426 -75 +mu-57/ 426 -57 diff --git a/GcmcTutorial/GcmcLj/top/GenerateTopologies.sh b/GcmcTutorial/GcmcLj/top/GenerateTopologies.sh new file mode 100755 index 0000000..352d11f --- /dev/null +++ b/GcmcTutorial/GcmcLj/top/GenerateTopologies.sh @@ -0,0 +1,38 @@ +#! /bin/bash + +EXPECTED_N_ARGS=3 +if [ $# -ne $EXPECTED_N_ARGS ]; then + echo "Input the correct amount of arguments!" + echo "Usage:" + echo "------" + echo "./GenerateTopologies.sh \"StartOfNRange\" \"EndOfNRange\" \"WInputN.top\"" + echo "Example: ./GenerateTopologies.sh1 430 W400.top" + echo "EXITING..." + exit 1 +fi + +NStart=$1 +NEnd=$2 +NInputFile=$3 +NInput=`echo $NInputFile | cut -d. -f1 | sed -e s/W//` + +declare -i N=$NStart +while [ $N -lt $NInput ] +do + NLines=`cat $NInputFile | wc -l` + head -$(($NLines-1)) $NInputFile > tmp.top + tail -1 $NInputFile | sed -e s/$NInput/$N/ >> tmp.top + mv tmp.top W$N.top + N=$N+1 +done +declare -i N=$(($NInput+1)) +while [ $N -le $NEnd ] +do + NLines=`cat $NInputFile | wc -l` + head -$(($NLines-1)) $NInputFile > tmp.top + tail -1 $NInputFile | sed -e s/$NInput/$N/ >> tmp.top + mv tmp.top W$N.top + N=$N+1 +done + +exit diff --git a/GcmcTutorial/GcmcLj/top/W400.top b/GcmcTutorial/GcmcLj/top/W400.top new file mode 100644 index 0000000..b060529 --- /dev/null +++ b/GcmcTutorial/GcmcLj/top/W400.top @@ -0,0 +1,14 @@ +; +;cg | MARTINI 2.1 +; + +; Force field: +#include "../itp/martini_v2.1.itp" + +[ system ] +; Name +water + +[ molecules ] +; Compound Nmol +W 400 diff --git a/GcmcTutorial/GcmcLj/tpr/GenerateTprs.sh b/GcmcTutorial/GcmcLj/tpr/GenerateTprs.sh new file mode 100755 index 0000000..1c63944 --- /dev/null +++ b/GcmcTutorial/GcmcLj/tpr/GenerateTprs.sh @@ -0,0 +1,11 @@ +#! /bin/bash + +for GroFile in `ls ../gro | grep \.gro` +do + BaseName=`echo $GroFile | cut -d. -f1` + grompp -f ../mdp/gcmc.mdp -c ../gro/$GroFile -p ../top/$BaseName.top -o $BaseName.tpr -maxwarn 1 + rm -f \#* + rm mdout.mdp +done + +exit diff --git a/GcmcTutorial/GcmcTutorial.aux b/GcmcTutorial/GcmcTutorial.aux index f9f3c1c..097fd11 100644 --- a/GcmcTutorial/GcmcTutorial.aux +++ b/GcmcTutorial/GcmcTutorial.aux @@ -1,2 +1,4 @@ \relax \@writefile{toc}{\contentsline {section}{\numberline {1}Downloading and installing the required files}{1}} +\@writefile{toc}{\contentsline {section}{\numberline {2}Calculation of the Lennard-Jones equation of state}{2}} +\@writefile{toc}{\contentsline {section}{\numberline {3}Analysis}{3}} diff --git a/GcmcTutorial/GcmcTutorial.tex b/GcmcTutorial/GcmcTutorial.tex index 11e8a20..f9f0ac6 100644 --- a/GcmcTutorial/GcmcTutorial.tex +++ b/GcmcTutorial/GcmcTutorial.tex @@ -34,15 +34,18 @@ simulations in the grand-canonical ensemble using the {\tt GROMACS} molecular simulation library via the {\tt GromPy} interface. After going through this tutorial you will be able to calculate an equation of state (EOS) of the -Lennard-Jones fluid. We assume that you use {\tt bash} shell of the Linux -operating system. If you are unfamiliar with some Linux commands, you can find -documentation in the corresponding {\tt man} pages or on the web. +Lennard-Jones (LJ) fluid. The system consists of mono-atomic water molceules +defined in the MARTINI force field. The intermolecular interactions between +such molecules are modelled using the Lennard-Jones potential only. We assume +that you use {\tt bash} shell of the Linux operating system. If you are unfamiliar +with some Linux commands, you can find documentation in the corresponding {\tt +man} pages or on the web. \end{abstract} \section{Downloading and installing the required files} \begin{itemize} - \item Go to your favorite working directory: {\tt \$WORK}, e.g. {\tt - \$WORK=/home/user/Simulation} + \item Go to your favorite working directory: {\tt \$WORK}, e.g. {\tt + WORK=/home/user/Simulation} \begin{itemize} \item[$\to$] {\tt cd \$WORK} \end{itemize} @@ -56,11 +59,102 @@ \section{Downloading and installing the required files} \end{itemize} \item Compile the {\tt GROMACS} source code \begin{itemize} - \item[$\to$] {\tt cd gromacs} - \item[$\to$] {\tt cd gromacs-4.0.5\_HYBRID} - \item[$\to$] {\tt something else} + \item[$\to$] {\tt cd gromacs} + \item[$\to$] {\tt cd gromacs-4.0.7} + \item[$\to$] {\tt tar -xzf ../gromacs-4.0.7-git.tar.gz} + \item[$\to$] {\tt cd gromacs-4.0.7-git} + \item[$\to$] {\tt patch -p1 < ../grompy\_4.0.7\_patch.diff} + \item[$\to$] {\tt ./bootstrap} + \item[$\to$] {\tt ./configure --enable-shared \char`\\ }\\ + {\tt --enable-grompy \char`\\} \\ + {\tt --prefix=\$PWD/install \char`\\}\\ + {\tt -CFLAGS \char`\"-O2 -fPIC\char`\"} + \item[$\to$] {\tt make -j 10} + \item[$\to$] {\tt make install} \end{itemize} + \item Save the {\tt GROMACS} install path to a variable + \begin{itemize} + \item[$\to$] {\tt GMXINSTALLDIR=\$PWD/install} + \end{itemize} + \item Go to the tutorial directory + \begin{itemize} + \item[$\to$] {\tt cd ../../../GcmcTutorial} + \end{itemize} + \item We now need to ``{\tt source}'' the {\tt GROMACS} and {\tt GromPy} + environment variables\\ + THIS NEEDS TO BE DONE WHENEVER YOU USE {\tt GromPy} IN A NEWLY OPENED + SHELL (SO REMEMBER THE {\tt GROMACS} INSTALLATION DIRECTORY)!! + \begin{itemize} + \item[$\to$] {\tt source \$GMXINSTALLDIR/bin/GMXRC} + \item[$\to$] {\tt source ./SourceGromPyEnv.sh \$GMXINSTALLDIR} + \end{itemize} +\end{itemize} + +\section{Calculation of the Lennard-Jones equation of state} +\begin{itemize} + \item The initial starting structure of the LJ system is an equilibrated one + containing $N=400$ LJ particles in a cubic box. Since it is equilibated, + there is no need to energy minimize the system. We will however equilibrate it using + MD for the desired temperature $T=773~\rm K$, just to be sure. This is done + in two steps: (1) equilibration using a small time step and (2) production at + the target time step $dt=0.02~\rm ps$. + \begin{itemize} + \item[$\to$] {\tt cd GcmcLj} + \item[$\to$] {\tt cd mdeq} + \item[$\to$] {\tt grompp -f ../mdp/mdeq.mdp \char`\\}\\ + {\tt -c ../initstructure/water.gro \char`\\}\\ + {\tt -p ../top/W400.top} + \item[$\to$] {\tt mdrun} + \item[$\to$] {\tt cd ../mdprod} + \item[$\to$] {\tt grompp -f ../mdp/mdprod.mdp \char`\\}\\ + {\tt -c ../mdeq/confout.gro \char`\\}\\ + {\tt -p ../top/W400.top \char`\\}\\ + {\tt -maxwarn 1} + \end{itemize} + \item To enable sampling of LJ particle numbers in the range $N\in [0,450]$, + we need to generate $450$ {\tt .tpr} files (for $N=0$ we do not need to + perform energy calculations {\tt ;-)}). We delete LJ particles from the equilibrated + {\tt W400.gro} structure to generate the $N\in [1,399]$ range of {\tt .gro} + files and then we add LJ particles for the $N\in [401,450]$ range of {\tt + .gro} files. Remember that {\tt GromPy} only needs an equilibrated + {\em starting} structure (one that does not contain particle overlaps). So as + long as we start {\tt GromPy} using a $N\in [1,400]$ structure, it will run fine. For + the higher $N$ range we can just generate structures by adding a new LJ + particle the last particle on top of e.g. the last particle. Before + generating the {\tt .tpr} files, we also need to generate 450 topology + ({\tt .top}) files. + \begin{itemize} + \item[$\to$] {\tt cd ../gro} + \item[$\to$] {\tt ln -sf ../mdprod/confout.gro ./W400.gro} + \item[$\to$] {\tt ./GenerateStartingStructures.sh 1 450 W400.gro} + \item[$\to$] {\tt cd ../top} + \item[$\to$] {\tt ./GenerateTopologies.sh 1 450 W400.top} + \item[$\to$] {\tt cd ../tpr} + \item[$\to$] {\tt ./GenerateTprs.sh 1 450} + \end{itemize} + \item We are now ready to perform grand-canonical simulations. In this + tutorial we will generate an equation of state in the $\mu VT$ ensemble at + $T=773~\rm K$ + \begin{itemize} + \item[$\to$] {\tt cd ../} + \item[$\to$] {\tt ./RunEos.sh} + \end{itemize} +\end{itemize} + +\section{Analysis} +\begin{itemize} + \item After performing the simulations, we will analyze the results by + generating block averages of the results. We postprocess the resulting file to obtain the equation of state: the + excess chemical potential as a function of density. + \begin{itemize} + \item[$\to$] {\tt DoBlockAveraging.sh} + \end{itemize} + \item Use your favorite plotting tool to check out the results in file + \newline {\tt \char`\"rho\_of\_mu\_with\_units.dat\char`\"}. If all works + well, the results should agree with the $NVT$ equation of state at $T=773~\rm K$. \end{itemize} +\section*{Disclaimer} +This code is NOT error-proof. Please notify us if you run into any problems. \end{document} \ No newline at end of file diff --git a/GcmcTutorial/SourceGromPyEnv.sh b/GcmcTutorial/SourceGromPyEnv.sh new file mode 100755 index 0000000..f693f81 --- /dev/null +++ b/GcmcTutorial/SourceGromPyEnv.sh @@ -0,0 +1,25 @@ +#! /bin/bash + +EXPECTED_N_ARGS=1 +if [ $# -ne $EXPECTED_N_ARGS ]; then + echo "Input the correct amount of arguments!" + echo "Usage:" + echo "------" + echo "source ./SourceGromPyEnv.sh \$GMXINSTALLDIR" + echo "EXITING..." +else + GMXINSTALLDIR=$1 + + source $GMXINSTALLDIR/bin/GMXRC + + LIBCPATH=`ldd $GMXINSTALLDIR/bin/mdrun | grep libc.so.6 | awk '{print $3}'` + GROMPY_LIBGMX=$GMXINSTALLDIR/lib/libgmx_grompy.so + GROMPY_LIBMD=$GMXINSTALLDIR/lib/libmd_grompy.so + GROMPY_LIBMDRUN=$GMXINSTALLDIR/lib/libmdrun_grompy.so + + export LIBCPATH + export GROMPY_LIBGMX + export GROMPY_LIBMD + export GROMPY_LIBMDRUN +fi + diff --git a/grompy/__init__.py b/grompy/__init__.py index 6d50c03..088a6f4 100644 --- a/grompy/__init__.py +++ b/grompy/__init__.py @@ -10,8 +10,9 @@ import sys - -libcname="/lib/libc.so.6" +libcname="/lib/libc.so.6" # default path, but is different in e.g. Ubuntu 11.10 +if environ.has_key("LIBCPATH"): + libcname=environ["LIBCPATH"] if environ.has_key("GROMPY_DOUBLE"): isdouble=True @@ -43,7 +44,7 @@ if environ.has_key("GROMPY_LIBMDRUN"): libmdrunname=environ["GROMPY_LIBMDRUN"] -libc = cdll.LoadLibrary(libcname) +libc = cdll.LoadLibrary(libcname) libmd = cdll.LoadLibrary(libmdname) libgmx = cdll.LoadLibrary(libgmxname) libmdrun = cdll.LoadLibrary(libmdrunname) diff --git a/testHybrid.py b/testHybrid.py index baf12bb..87cdc78 100755 --- a/testHybrid.py +++ b/testHybrid.py @@ -1,3 +1,5 @@ +#! /usr/bin/env python + #from ctypes import c_char_p import sys @@ -24,4 +26,5 @@ else: bUseNrgGrps = False from grompy.Hybrid import * + print "joh" hybrid(Mu,NStart,NMax,NMin,TprDir,MolName)