Tutorial2 script - Revision history

Miguel Caro at 13:33, 24 April 2017

2017-04-24T13:33:28Z

Miguel Caro at 11:50, 24 April 2017

2017-04-24T11:50:12Z

Miguel Caro at 16:08, 21 April 2017

2017-04-21T16:08:58Z

Miguel Caro at 15:47, 21 April 2017

2017-04-21T15:47:27Z

Miguel Caro at 15:46, 21 April 2017

2017-04-21T15:46:05Z

Miguel Caro at 15:38, 21 April 2017

2017-04-21T15:38:32Z

Miguel Caro at 15:02, 21 April 2017

2017-04-21T15:02:04Z

Miguel Caro at 12:18, 21 April 2017

2017-04-21T12:18:45Z

Miguel Caro at 12:17, 21 April 2017

2017-04-21T12:17:18Z

Miguel Caro at 12:00, 21 April 2017

2017-04-21T12:00:37Z

@@ Line 12: / Line 12: @@
   tau_t=0.1; ref_t=298.
   else
-  mols="MET    200\nSOL    400"
+  mols="SOL    200\nMET    400"
-  tc_grps="MOL SOL"
+  tc_grps="SOL MOL"
-  energygrps="MOL SOL"
+  energygrps="SOL MOL"
   tau_t="0.1 0.1"; ref_t="298. 298"
   fi
@@ Line 31: / Line 31: @@
   echo -e $mols >> topol.top
-  awk -v tc_grps=$tc_grps -v energygrps=$energygrps -v tau_t=$tau_t -v ref_t=$ref_t \
+  awk -v tc_grps="$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"}

@@ Line 11: / Line 11: @@
   energygrps="SOL"
   tau_t=0.1; ref_t=298.
-  elif [ $i == "mixture"* ]; then
+  else
   mols="MET    200\nSOL    400"
   tc_grps="MOL SOL"

@@ Line 30: / Line 30: @@
   eof
   echo -e $mols >> topol.top
-−
   awk -v tc_grps=$tc_grps -v energygrps=$energygrps -v tau_t=$tau_t -v ref_t=$ref_t \
   '{if($1 == "Tcoupl"){print "Tcoupl = v-rescale"}

@@ Line 3: / Line 3: @@
   if [ $i == "pure_methanol" ]; then
   mols="MET    400"
-  tc_grps="MET"
+  tc_grps="MOL"
-  energygrps="MET"
+  energygrps="MOL"
   tau_t=0.1; ref_t=298.
   elif [ $i == "pure_water" ]; then
@@ Line 13: / Line 13: @@
   elif [ $i == "mixture"* ]; then
   mols="MET    200\nSOL    400"
-  tc_grps="MET SOL"
+  tc_grps="MOL SOL"
-  energygrps="MET SOL"
+  energygrps="MOL SOL"
   tau_t="0.1 0.1"; ref_t="298. 298"
   fi

@@ Line 2: / Line 2: @@
   if [ $i == "pure_methanol" ]; then
-  mols="MOL    400"
+  mols="MET    400"
-  tc_grps="MOL"
+  tc_grps="MET"
-  energygrps="MOL"
+  energygrps="MET"
   tau_t=0.1; ref_t=298.
   elif [ $i == "pure_water" ]; then
@@ Line 12: / Line 12: @@
   tau_t=0.1; ref_t=298.
   elif [ $i == "mixture"* ]; then
-  mols="MOL    200\nSOL    400"
+  mols="MET    200\nSOL    400"
-  tc_grps="MOL SOL"
+  tc_grps="MET SOL"
-  energygrps="MOL SOL"
+  energygrps="MET SOL"
   tau_t="0.1 0.1"; ref_t="298. 298"
   fi

@@ Line 53: / Line 53: @@
   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`
+  gnuplot -e "set fit quiet; fit[250:500] a 'box' via a; set print 'l'; print a"
   awk -v l=$l '{if(NR==2403){printf "   %.5f   %.5f   %.5f", l, l, l} else {print $0}}' md.gro > temp; mv temp md.gro

@@ Line 1: / Line 1: @@
- 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
+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
+if [ $i == "pure_methanol" ]; then
- sol=0; met=400
+sol=0; met=400
- elif [ $i == "pure_water" ]; then
+tc_grps="MOL"
- sol=800; met=0
+energygrps="MOL"
- elif [ $i == "mixture"* ]; then
+tau_t=0.1; ref_t=298.
- sol=400; met=200
+elif [ $i == "pure_water" ]; then
- fi
+sol=800; met=0
+tc_grps="SOL"
- cat>topol.top<<eof
+energygrps="SOL"
- #include "oplsaa.ff/forcefield.itp"
+tau_t=0.1; ref_t=298.
- #include "oplsaa.ff/spce.itp"
+elif [ $i == "mixture"* ]; then
- #include "methanol.itp"
+sol=400; met=200
+tc_grps="MOL SOL"
- [ system ]
+energygrps="MOL SOL"
- Water+methanol
+tau_t="0.1 0.1"; ref_t="298. 298"
 fi
- [ molecules ]
- ; name  number
+cat>topol.top<<eof
- SOL       $sol
+#include "oplsaa.ff/forcefield.itp"
- MET       $met
+#include "oplsaa.ff/spce.itp"
- eof
+#include "methanol.itp"
-−
 [ system ]
- awk '{if($1 == "Tcoupl"){print "Tcoupl = v-rescale"}
+Water+methanol
    else if($1 == "Pcoupl"){print "Pcoupl = Berendsen"}
    else if($1 == "Pcoupl"){print"gen_vel = yes"}
@@ Line 30: / Line 40: @@
    else if($1 == "nstxout"){print "nstxout = 1000"}
    else if($1 == "nstvout"){print "nstvout = 1000"}
    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 grompp -f em.mdp -c ${i}.gro -p topol.top -o em.tpr
- gmx mdrun -v -deffnm em
+gmx mdrun -v -deffnm em
-−
- gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr
+gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr
- gmx mdrun -v -deffnm md
+gmx mdrun -v -deffnm md
-−
- echo "Box-X" | gmx energy -f md.edr -o density.xvg; grep -v "\@" density.xvg | grep -v "\#" > box
+echo "Box-X" | gmx energy -f md.edr -o density.xvg; grep -v "\@" density.xvg | grep -v "\#" > box
- l=`echo 'set fit quiet; fit[250:*] a "box" via a; print a' | gnuplot`
+l=`echo 'set fit quiet; fit[250:*] a "box" via a; print a' | gnuplot`
-−
- awk -v l=$l '{if(NR==2403){printf "   %.5f   %.5f   %.5f", l, l, l} else {print $0}}' md.gro > temp; mv temp md.gro
+awk -v l=$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"}
+awk '{if($1 == "Tcoupl"){print "Tcoupl = nose-hoover"}
-  else if($1 == "Pcoupl"){print "Pcoupl = no"}
+ else if($1 == "Pcoupl"){print "Pcoupl = no"}
-  else if($1 == "Pcoupl"){print"gen_vel = no"}
+ else if($1 == "Pcoupl"){print"gen_vel = no"}
-  else {print $0}}' md.mdp > temp; cp temp md.mdp
+ else {print $0}}' md.mdp > temp; cp temp md.mdp
-−
- cp md.gro NPT_${i}.gro
+cp md.gro NPT_${i}.gro
- gmx grompp -f md.mdp -c NPT_${i}.gro -p topol.top -o md.tpr
+gmx grompp -f md.mdp -c NPT_${i}.gro -p topol.top -o md.tpr
- gmx mdrun -v -deffnm md
+gmx mdrun -v -deffnm md
-−
- cp md.gro NVT_${i}.gro
+cp md.gro NVT_${i}.gro
-−
- awk '{if($1 == "nsteps"){print "nsteps = 10000"}
+awk '{if($1 == "nsteps"){print "nsteps = 10000"}
-  else if($1 == "nstxout"){print "nstxout = 2"}
+ else if($1 == "nstxout"){print "nstxout = 2"}
-  else if($1 == "nstvout"){print "nstvout = 2"}
+ else if($1 == "nstvout"){print "nstvout = 2"}
-  else {print $0}}' md.mdp > temp; cp temp md.mdp
+ 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 grompp -f md.mdp -c NVT_${i}.gro -p topol.top -o md.tpr
- gmx mdrun -v -deffnm md
+gmx mdrun -v -deffnm md
-−
- echo "0" | gmx trjconv -f md.trr -s md.tpr -o traj_${i}.gro -dt 0.004 -ndec 5 -vel
+echo "0" | gmx trjconv -f md.trr -s md.tpr -o traj_${i}.gro -dt 0.004 -ndec 5 -vel
-−
- done
+done