The job.sh script I provide for running these calculations will create the following directory hierarchy:

Lambda_0/
Lambda_0/EM/
Lambda_0/NVT/
Lambda_0/NPT/
Lambda_0/Production_MD/

This way, all steps in the workflow are executed within a single directory for each value of init_lambda_state. I find this to be a convenient way to organize the jobs and their output.

The script also assumes that the .mdp files are also organized hierarchically within some directory $MDP, which is set as an environment variable in the script:

$MDP/
$MDP/EM/
$MDP/NVT/
$MDP/NPT/
$MDP/Production_MD/

As described before, energy minimization will be conducted using the steepest descent method. The relevant section in the job.sh script is:

mkdir Lambda_$LAMBDA
cd Lambda_$LAMBDA

coorfile=$FREE_ENERGY/etoh_solv.gro
if [[ $i -gt 1 ]]; then
    coorfile=$FREE_ENERGY/Lambda_$prevlambda/Production_MD/md$prevlambda.gro
fi

#################################
# ENERGY MINIMIZATION 1: STEEP  #
#################################
echo "Starting minimization for lambda = $LAMBDA..."

mkdir EM
cd EM

# Iterative calls to grompp and mdrun to run the simulations

gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $coorfile  -p $FREE_ENERGY/topol.top -o min$LAMBDA.tpr

gmx mdrun -deffnm min$LAMBDA

echo "Minimization complete."

#####################
# NVT EQUILIBRATION #
#####################
echo "Starting constant volume equilibration..."

cd ../
mkdir NVT
cd NVT

gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/topol.top -o nvt$LAMBDA.tpr

gmx mdrun -deffnm nvt$LAMBDA

echo "Constant volume equilibration complete."

#####################
# NPT EQUILIBRATION #
#####################
echo "Starting constant pressure equilibration..."

cd ../
mkdir NPT
cd NPT

gmx grompp -f $MDP/npt_$LAMBDA.mdp -c ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/topol.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr

gmx mdrun -deffnm npt$LAMBDA

echo "Constant pressure equilibration complete."

#################
# PRODUCTION MD #
#################
echo "Starting production MD simulation..."

cd ../
mkdir Production_MD
cd Production_MD

gmx grompp -f $MDP/md_$LAMBDA.mdp -c ../NPT/npt$LAMBDA.gro -p $FREE_ENERGY/topol.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr

gmx mdrun -deffnm md$LAMBDA

echo "Production MD complete."