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comparison alchemical_run/gmx_fep.sh @ 0:5f136e371f44 draft

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit 4c75f8d26505d221d4144f4ae7d2fb7698fbe4ab"
author chemteam
date Mon, 18 Nov 2019 09:52:20 -0500
parents
children c1fa72716efc
comparison
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-1:000000000000 0:5f136e371f44
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 set -e
16
17 for i in `seq 0 $lam`
18 do
19 cp em_steep.mdp em_steep_$i.mdp
20 sed -i "s/%L%/$i/" em_steep_$i.mdp
21 cp nvt.mdp nvt_$i.mdp
22 sed -i "s/%L%/$i/" nvt_$i.mdp
23 cp npt.mdp npt_$i.mdp
24 sed -i "s/%L%/$i/" npt_$i.mdp
25 cp md.mdp md_$i.mdp
26 sed -i "s/%L%/$i/" md_$i.mdp
27 done
28 mv *.mdp $MDP
29
30 for (( i=0; i<$iter; i++ ))
31 do
32 LAMBDA=$i
33
34 # A new directory will be created for each value of lambda
35
36 mkdir Lambda_$LAMBDA
37 cd Lambda_$LAMBDA
38
39 # _______ ENERGY MINIMIZATION STEEP _______
40
41 echo "Starting minimization for lambda = $LAMBDA..."
42
43 mkdir EM
44 cd EM
45
46 # Iterative calls to grompp and mdrun to run the simulations
47
48 gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr
49
50 gmx mdrun -deffnm min$LAMBDA
51
52 sleep 10
53
54
55 # _______ NVT EQUILIBRATION _______
56
57 echo "Starting constant volume equilibration..."
58
59 cd ../
60 mkdir NVT
61 cd NVT
62
63 gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr
64
65 gmx mdrun -deffnm nvt$LAMBDA
66
67 echo "Constant volume equilibration complete."
68
69 sleep 10
70
71 # _______ NPT EQUILIBRATION _______
72
73 echo "Starting constant pressure equilibration..."
74
75 cd ../
76 mkdir NPT
77 cd NPT
78
79 gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
80
81 gmx mdrun -deffnm npt$LAMBDA
82
83 echo "Constant pressure equilibration complete."
84
85 sleep 10
86
87 # ________ PRODUCTION MD ___________
88
89 echo "Starting production MD simulation..."
90
91 cd ../
92 mkdir Production_MD
93 cd Production_MD
94
95 gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
96
97 gmx mdrun -deffnm md$LAMBDA
98
99 echo "Production MD complete."
100
101 # End
102 echo "Ending. Job completed for lambda = $LAMBDA"
103
104 cd $FREE_ENERGY
105 done
106
107 cp Lambda_*/Production_MD/*.xvg data/
108 tar cf data.tar data/
109
110 cp Lambda_*/Production_MD/*.trr traj/
111 tar cf traj.tar traj/
112
113 exit;
114
115