# HG changeset patch
# User chemteam
# Date 1575211672 18000
# Node ID c1fa72716efc5ed07e9fd977b4f5635bb950cd5d
# Parent  5f136e371f4467e591bac7096a79b300e08e11cb
"planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/tools/free_energy commit eefe89bfcd6c3e98f4e774e508ad0659dcc2f65c"

diff -r 5f136e371f44 -r c1fa72716efc alchemical_run/gmx_fep.sh
--- a/alchemical_run/gmx_fep.sh	Mon Nov 18 09:52:20 2019 -0500
+++ b/alchemical_run/gmx_fep.sh	Sun Dec 01 09:47:52 2019 -0500
@@ -47,7 +47,7 @@
 
     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$LAMBDA
+    gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm min$LAMBDA
 
     sleep 10
 
@@ -62,7 +62,7 @@
 
     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$LAMBDA
+    gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm nvt$LAMBDA
 
     echo "Constant volume equilibration complete."
 
@@ -78,7 +78,7 @@
 
     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$LAMBDA
+    gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm npt$LAMBDA
 
     echo "Constant pressure equilibration complete."
 
@@ -94,7 +94,7 @@
 
     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$LAMBDA
+    gmx mdrun -nt "${GALAXY_SLOTS:-4}" -deffnm md$LAMBDA
 
     echo "Production MD complete."
 
@@ -112,4 +112,3 @@
 
 exit;
 
-