updated input

Author: simongravelle

level3/solvation-energy/preparation/icpRun.sh

@@ -0,0 +1,18 @@
+#!/bin/sh
+set -e 
+
+export GMX_MAXBACKUP=-1
+
+gmx=/home/simon/Softwares/gromacs-2024.2/build/bin/gmx
+
+${gmx} trjconv -f FJEW_allatom_optimised_geometry.pdb -s FJEW_allatom_optimised_geometry.pdb -o hbc.gro -box 3.5 3.5 3.5 -center << EOF
+	0
+	0
+EOF
+
+${gmx} grompp -f inputs/min.mdp -c solvated.gro -p topol.top -o min -pp min -po min -maxwarn 1
+${gmx} mdrun -v -deffnm min -nt 8
+${gmx} grompp -f inputs/nvt.mdp -c min.gro -p topol.top -o nvt -pp nvt -po nvt -maxwarn 1
+${gmx} mdrun -v -deffnm nvt -nt 8
+${gmx} grompp -f inputs/npt.mdp -c nvt.gro -p topol.top -o npt -pp npt -po npt -maxwarn 1
+${gmx} mdrun -v -deffnm npt -nt 8