update gromacs/wham2d example for dialanine

examples/data/plumed.dat

@@ -0,0 +1,13 @@
+# set up two variables for Phi and Psi dihedral angles 
+phi: TORSION ATOMS=5,7,9,15
+psi: TORSION ATOMS=7,9,15,17
+#
+# Impose an umbrella potential on CV 1 and CV 2
+# with a spring constant of 500 kjoule/mol
+# at fixed points on the Ramachandran plot
+#
+restraint-phi: RESTRAINT ARG=phi KAPPA=100 AT=LAMBDA1
+restraint-psi: RESTRAINT ARG=psi KAPPA=100 AT=LAMBDA2
+
+# monitor the two variables and the bias potential from the two restraints
+PRINT STRIDE=10 ARG=phi,psi,restraint-phi.bias,restraint-psi.bias FILE=COLVAR UPDATE_FROM=50

examples/data/sim.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+lambda1=$1
+lambda2=$2
+FOLDER="./tmp/simulations/sim_${lambda1}_${lambda2}"
+
+
+if [ -f $FOLDER/topol.gro ]; then
+	echo "$FOLDER exists"
+	exit 0
+fi
+
+mkdir -p $FOLDER
+cp data/plumed.dat $FOLDER
+cp data/topol.tpr $FOLDER
+sed -i -e "s/LAMBDA1/${lambda1}/g" $FOLDER/plumed.dat
+sed -i -e "s/LAMBDA2/${lambda2}/g" $FOLDER/plumed.dat
+
+cd $FOLDER
+source /usr/local/gromacs/bin/GMXRC
+gmx --quiet mdrun -deffnm topol -plumed plumed.dat -nsteps 100000 2>&1
+cd ../..
+