--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/alchemical_run/gmx_fep.sh	Mon Nov 11 13:20:39 2019 -0500
@@ -0,0 +1,114 @@
+#!/bin/bash
+
+# _________ read inputs from the galaxy wrapper and define some variables ____________ 
+
+lam=$1
+iter=$((lam+1))
+
+mkdir MDP
+mkdir data
+mkdir traj
+ 
+FREE_ENERGY=`pwd`
+MDP=$FREE_ENERGY/MDP
+
+
+for i in `seq 0 $lam`
+ do
+   cp em_steep.mdp em_steep_$i.mdp
+   sed -i "s/%L%/$i/" em_steep_$i.mdp
+   cp nvt.mdp nvt_$i.mdp
+   sed -i "s/%L%/$i/" nvt_$i.mdp 
+   cp npt.mdp npt_$i.mdp
+   sed -i "s/%L%/$i/" npt_$i.mdp 
+   cp md.mdp md_$i.mdp
+   sed -i "s/%L%/$i/" md_$i.mdp  
+ done
+mv *.mdp $MDP
+
+for (( i=0; i<$iter; i++ ))
+do
+    LAMBDA=$i
+
+    # A new directory will be created for each value of lambda 
+
+    mkdir Lambda_$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
+
+    gmx grompp -f $MDP/em_steep_$LAMBDA.mdp -c $FREE_ENERGY/morph.gro -p $FREE_ENERGY/morph.top -o min$LAMBDA.tpr
+
+    gmx mdrun -deffnm min$LAMBDA
+
+    sleep 10
+
+
+# _______ 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 $FREE_ENERGY/morph.top -o nvt$LAMBDA.tpr
+
+    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 ../NVT/nvt$LAMBDA.gro -p $FREE_ENERGY/morph.top -t ../NVT/nvt$LAMBDA.cpt -o npt$LAMBDA.tpr
+
+    gmx mdrun -deffnm npt$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 $FREE_ENERGY/morph.top -t ../NPT/npt$LAMBDA.cpt -o md$LAMBDA.tpr
+
+    gmx mdrun -deffnm md$LAMBDA
+
+    echo "Production MD complete."
+
+    # End
+    echo "Ending. Job completed for lambda = $LAMBDA"
+
+    cd $FREE_ENERGY
+done
+
+cp Lambda_*/Production_MD/*.xvg data/
+tar cf data.tar data/
+
+cp Lambda_*/Production_MD/*.trr traj/
+tar cf traj.tar traj/
+
+exit;
+
+