FEP Job file Gromacs

Lambda.sh

#!/bin/bash
#BSUB -o .                       ## requests outfile be generated
#BSUB -a openmpi
#BSUB -q shared                  ## specify queue to run on, shared = default
#BSUB -J ACH           ## job-name
#BSUB -W 24:00                   ## walltime <HH:MM>= 24 hrs
#BSUB -n 8  
#BSUB -R "rusage[mem=50000]"     ## memory limit= MB count only (1024MB = 1GB)
module load Apps/Gromacs

# Set some environment variables 
FREE_ENERGY=$PWD
#/home/justin/Free_Energy
echo "Free energy home directory set to $FREE_ENERGY"

MDP=$FREE_ENERGY/MDP
EM=$MDP/EM
NVT=$MDP/NVT
NPT=$MDP/NPT
PROD=$MDP/Prod_MD
SYSTEM=$FREE_ENERGY/SYSTEM
echo ".mdp files are stored in $MDP"

LAMBDA=X

# A new directory will be created for each value of lambda and
# at each step in the workflow for maximum organization.

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

echo "Starting production MD simulation..."
grompp -f $EM/NMA_EM.$LAMBDA.mdp -c $SYSTEM/NMA.gro -p $SYSTEM/NMA.top -o NMA_EM.$LAMBDA.tpr -maxwarn 8
mpirun.lsf mdrun_mpi  -deffnm NMA_EM.$LAMBDA
grompp -f $NVT/NMA_NVT.$LAMBDA.mdp -c NMA_EM.$LAMBDA.gro -p $SYSTEM/NMA.top -o NMA_NVT.$LAMBDA.tpr -maxwarn 8
mpirun.lsf mdrun_mpi  -deffnm NMA_NVT.$LAMBDA
grompp -f $NPT/NMA_NPT.$LAMBDA.mdp -c NMA_NVT.$LAMBDA.gro -p $SYSTEM/NMA.top -o NMA_NPT.$LAMBDA.tpr -maxwarn 8
mpirun.lsf mdrun_mpi  -deffnm NMA_NPT.$LAMBDA
grompp -f $PROD/NMA.$LAMBDA.mdp -c NMA_NPT.$LAMBDA.gro -p $SYSTEM/NMA.top -o NMA.$LAMBDA.tpr -maxwarn 8
mpirun.lsf mdrun_mpi  -deffnm NMA.$LAMBDA -dhdl NMA.$LAMBDA.dhdl.xvg
echo "Production MD complete."
# End
echo "Ending. Job completed for lambda = $LAMBDA"