Tutorial2 script

for i in "pure_methanol" "pure_water" "mixture_1" "mixture_2" "mixture_3" "mixture_4" "mixture_5" "mixture_6" "mixture_7" "mixture_8" "mixture_9" "mixture_10"; do

if [ $i == "pure_methanol" ]; then sol=0; met=400 tc_grps="MOL" energygrps="MOL" tau_t=0.1; ref_t=298. elif [ $i == "pure_water" ]; then sol=800; met=0 tc_grps="SOL" energygrps="SOL" tau_t=0.1; ref_t=298. elif [ $i == "mixture"* ]; then sol=400; met=200 tc_grps="MOL SOL" energygrps="MOL SOL" tau_t="0.1 0.1"; ref_t="298. 298" fi

cat>topol.top<<eof

1. include "oplsaa.ff/forcefield.itp"
2. include "oplsaa.ff/spce.itp"
3. include "methanol.itp"

[ system ] Water+methanol

[ molecules ]

name number

SOL $sol MET $met eof

awk -v tc_grps=$tc_grps -v energygrps=$energygrps -v tau_t=$tau_t -v ref_t=$ref_t \ '{if($1 == "Tcoupl"){print "Tcoupl = v-rescale"}

 else if($1 == "Pcoupl"){print "Pcoupl = Berendsen"}
 else if($1 == "Pcoupl"){print"gen_vel = yes"}
 else if($1 == "nsteps"){print "nsteps = 250000"}
 else if($1 == "nstxout"){print "nstxout = 1000"}
 else if($1 == "nstvout"){print "nstvout = 1000"}
 else if($1 == "tc-grps"){print "tc-grps =", tc_grps}
 else if($1 == "energygrps"){print "energygrps =", energygrps}
 else if($1 == "tau_t"){print "tau_t =", tau_t}
 else if($1 == "ref_t"){print "ref_t =", ref_t}
 else {print $0}}' md.mdp > temp; cp temp md.mdp

gmx grompp -f em.mdp -c ${i}.gro -p topol.top -o em.tpr gmx mdrun -v -deffnm em

gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr gmx mdrun -v -deffnm md

echo "Box-X" | gmx energy -f md.edr -o density.xvg; grep -v "\@" density.xvg | grep -v "\#" > box l=`echo 'set fit quiet; fit[250:*] a "box" via a; print a' | gnuplot`

awk -v l=$l '{if(NR==2403){printf "  %.5f  %.5f  %.5f", l, l, l} else {print $0}}' md.gro > temp; mv temp md.gro

awk '{if($1 == "Tcoupl"){print "Tcoupl = nose-hoover"}

else if($1 == "Pcoupl"){print "Pcoupl = no"}
else if($1 == "Pcoupl"){print"gen_vel = no"}
else {print $0}}' md.mdp > temp; cp temp md.mdp

cp md.gro NPT_${i}.gro gmx grompp -f md.mdp -c NPT_${i}.gro -p topol.top -o md.tpr gmx mdrun -v -deffnm md

cp md.gro NVT_${i}.gro

awk '{if($1 == "nsteps"){print "nsteps = 10000"}

else if($1 == "nstxout"){print "nstxout = 2"}
else if($1 == "nstvout"){print "nstvout = 2"}
else {print $0}}' md.mdp > temp; cp temp md.mdp

gmx grompp -f md.mdp -c NVT_${i}.gro -p topol.top -o md.tpr gmx mdrun -v -deffnm md

echo "0" | gmx trjconv -f md.trr -s md.tpr -o traj_${i}.gro -dt 0.004 -ndec 5 -vel

done