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comparison alchemical_run/gmx_fep.sh @ 2:c1bcdba99bb3 draft default tip

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"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c"
author chemteam
date Sun, 01 Dec 2019 09:47:35 -0500
parents 453311042f29
children
comparison
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1:453311042f29 2:c1bcdba99bb3
45 45
46 # Iterative calls to grompp and mdrun to run the simulations 46 # Iterative calls to grompp and mdrun to run the simulations
47 47
48 gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr 48 gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr
49 49
50 gmx mdrun -deffnm min$LAMBDA 50 gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm min$LAMBDA
51 51
52 sleep 10 52 sleep 10
53 53
54 54
55 # _______ NVT EQUILIBRATION _______ 55 # _______ NVT EQUILIBRATION _______
60 mkdir NVT 60 mkdir NVT
61 cd NVT 61 cd NVT
62 62
63 gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr 63 gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr
64 64
65 gmx mdrun -deffnm nvt$LAMBDA 65 gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm nvt$LAMBDA
66 66
67 echo "Constant volume equilibration complete." 67 echo "Constant volume equilibration complete."
68 68
69 sleep 10 69 sleep 10
70 70
76 mkdir NPT 76 mkdir NPT
77 cd NPT 77 cd NPT
78 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 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$LAMBDA.tpr
80 80
81 gmx mdrun -deffnm npt$LAMBDA 81 gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm npt$LAMBDA
82 82
83 echo "Constant pressure equilibration complete." 83 echo "Constant pressure equilibration complete."
84 84
85 sleep 10 85 sleep 10
86 86
92 mkdir Production_MD 92 mkdir Production_MD
93 cd Production_MD 93 cd Production_MD
94 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 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$LAMBDA.tpr
96 96
97 gmx mdrun -deffnm md$LAMBDA 97 gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm md$LAMBDA
98 98
99 echo "Production MD complete." 99 echo "Production MD complete."
100 100
101 # End 101 # End
102 echo "Ending. Job completed for lambda = $LAMBDA" 102 echo "Ending. Job completed for lambda = $LAMBDA"
110 cp Lambda_*/Production_MD/*.trr traj/ 110 cp Lambda_*/Production_MD/*.trr traj/
111 tar cf traj.tar traj/ 111 tar cf traj.tar traj/
112 112
113 exit; 113 exit;
114 114
115