#!/bin/bash
label="2.5mM"
#
# CLEAN
cd /Users/mccallum/Res/Martini/CMC/TTA/BzO/$label
rm -rf \#* ${label}-run.??? ${label}-eq.???

# added -ntmpi 1 for M# Apple silicon
 gmx grompp -p ${label}_System.top -c ${label}_System.gro -f ../minimization.mdp -o ${label}-min.tpr -po ${label}-min.mdp 
 gmx mdrun -ntmpi 1 -v -deffnm ${label}-min >> mdrun.log 2>&1

gmx grompp -p ${label}_System.top -c ${label}-min.gro -f ../martini_eq.mdp -o ${label}-eq.tpr -po ${label}-eq.mdp -maxwarn 1
gmx mdrun -ntmpi 4 -v -deffnm ${label}-eq  >> mdrun.log 2>&1

gmx grompp -p ${label}_System.top -c ${label}-eq.gro    -f ../martini_md.mdp -o ${label}-run.tpr -po ${label}-run.mdp -maxwarn 1
gmx mdrun -ntmpi 4 -v -deffnm ${label}-run >> mdrun.log 2>&1