run_lambda.sh

#!/bin/bash

while getopts v:u:r:n:l:d; flag
do
    case "${flag}" in
        v) SOLV_NAME=${OPTARG};;
        u) SOLU_NAME=${OPTARG};;
        r) RES_NAME=${OPTARG};;
        n) NUM_MOL=${OPTARG};;
        l) BOX_LEN=${OPTARG};;
        d) LAMBDA=${OPTARG};;
    esac
done

#go into hfc_ops/general_mdp
export HOMEDIR=$PWD
echo "solvname and soluname"
echo ${SOLV_NAME} ${SOLU_NAME}

#docker environment variables
HOMEDIR=/container_home
SOLV_NAME=methanol
SOLU_NAME=ch3f
LAMBDA=0
FREE_ENERGY=${HOMEDIR}/solvate
LOCAL_WORKDIR=/home/pablo/proj/hfc_docker/${SOLV_NAME}/${SOLU_NAME}
#-----These are files that will be "inside the container"
WORKDIR=${HOMEDIR}/full_test/Lambda_${LAMBDA}
echo "Free energy home directory set to $FREE_ENERGY"
MDP=${HOMEDIR}/general_mdp
echo ".mdp files are stored in $MDP"

GMX="docker run -v ${LOCAL_WORKDIR}:/container_home -w /container_home -it gromacs/gromacs gmx"

mkdir -p ${LOCAL_WORKDIR}
cd ${LOCAL_WORKDIR}

# 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

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

mkdir EM
cd EM

# Iterative calls to grompp and mdrun to run the simulations

echo $GMX grompp -f $MDP/min_$LAMBDA.mdp -c $FREE_ENERGY/solvated.gro -p $FREE_ENERGY/solvated_top.top -o $WORKDIR/EM/min$LAMBDA.tpr -maxwarn 1
# $GMX grompp -f $MDP/min_$LAMBDA.mdp -c $FREE_ENERGY/solvated.gro -p $FREE_ENERGY/solvated_top.top -o min$LAMBDA.tpr -maxwarn 1
$GMX mdrun -deffnm $WORKDIR/EM/min$LAMBDA

# sleep 10

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

# cd ../
# mkdir NVT
# cd NVT

# $GMX/gmx grompp -f $MDP/nvt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/solvated_top.top -o nvt$LAMBDA.tpr
# $GMX/gmx mdrun -deffnm nvt$LAMBDA
# echo "Constant volume equilibration complete."

# sleep 10

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

# cd ../
# mkdir NPT
# cd NPT

# $GMX grompp -f $MDP/npt_$LAMBDA.mdp -c ../EM/min$LAMBDA.gro -p $FREE_ENERGY/solvated_top.top -o npt$LAMBDA.tpr -maxwarn 1
# $GMX mdrun -deffnm npt$LAMBDA
# echo "Constant pressure equilibration complete."

# sleep 10

# #################
# # 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 $FREE_ENERGY/solvated_top.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr -maxwarn 1
# $GMX mdrun -deffnm md$LAMBDA
# echo "Production MD complete."

# #################
# #      END      #
# #################
# echo "-------------------------------------Ending. Job completed for lambda = $LAMBDA -------------------------------------"
# cd $HOMEDIR
# exit;