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comparison alchemical_run/gmx_fep.sh @ 0:19d1d4c30402 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit b73986b131478d51e119de635fea5bd752c23b99"
author chemteam
date Mon, 11 Nov 2019 13:20:39 -0500
parents
children 453311042f29
comparison
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-1:000000000000 0:19d1d4c30402
1 #!/bin/bash
2
3 # _________ read inputs from the galaxy wrapper and define some variables ____________
4
5 lam=$1
6 iter=$((lam+1))
7
8 mkdir MDP
9 mkdir data
10 mkdir traj
11
12 FREE_ENERGY=`pwd`
13 MDP=$FREE_ENERGY/MDP
14
15
16 for i in `seq 0 $lam`
17 do
18 cp em_steep.mdp em_steep_$i.mdp
19 sed -i "s/%L%/$i/" em_steep_$i.mdp
20 cp nvt.mdp nvt_$i.mdp
21 sed -i "s/%L%/$i/" nvt_$i.mdp
22 cp npt.mdp npt_$i.mdp
23 sed -i "s/%L%/$i/" npt_$i.mdp
24 cp md.mdp md_$i.mdp
25 sed -i "s/%L%/$i/" md_$i.mdp
26 done
27 mv *.mdp $MDP
28
29 for (( i=0; i<$iter; i++ ))
30 do
31 LAMBDA=$i
32
33 # A new directory will be created for each value of lambda
34
35 mkdir Lambda_$LAMBDA
36 cd Lambda_$LAMBDA
37
38 # _______ ENERGY MINIMIZATION STEEP _______
39
40 echo "Starting minimization for lambda = $LAMBDA..."
41
42 mkdir EM
43 cd EM
44
45 # Iterative calls to grompp and mdrun to run the simulations
46
47 gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr
48
49 gmx mdrun -deffnm min$LAMBDA
50
51 sleep 10
52
53
54 # _______ NVT EQUILIBRATION _______
55
56 echo "Starting constant volume equilibration..."
57
58 cd ../
59 mkdir NVT
60 cd NVT
61
62 gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr
63
64 gmx mdrun -deffnm nvt$LAMBDA
65
66 echo "Constant volume equilibration complete."
67
68 sleep 10
69
70 # _______ NPT EQUILIBRATION _______
71
72 echo "Starting constant pressure equilibration..."
73
74 cd ../
75 mkdir NPT
76 cd NPT
77
78 gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
79
80 gmx mdrun -deffnm npt$LAMBDA
81
82 echo "Constant pressure equilibration complete."
83
84 sleep 10
85
86 # ________ PRODUCTION MD ___________
87
88 echo "Starting production MD simulation..."
89
90 cd ../
91 mkdir Production_MD
92 cd Production_MD
93
94 gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
95
96 gmx mdrun -deffnm md$LAMBDA
97
98 echo "Production MD complete."
99
100 # End
101 echo "Ending. Job completed for lambda = $LAMBDA"
102
103 cd $FREE_ENERGY
104 done
105
106 cp Lambda_*/Production_MD/*.xvg data/
107 tar cf data.tar data/
108
109 cp Lambda_*/Production_MD/*.trr traj/
110 tar cf traj.tar traj/
111
112 exit;
113
114