#!/bin/bash
#
# use: ./dry_martini.sh label stage (for example label = 1.0mM, stage = run)
label=$1
stage=$2
#
# should put something here to convert xx_System.top to xx_vis.top
#
martiniglass -p ${label}_vis.top -f ${label}-${stage}.gro
gmx trjconv -f ${label}-${stage}.gro -s ${label}-${stage}.gro -n index.ndx -o ${label}-${stage}-vis.gro
gmx trjconv -f ${label}-${stage}.xtc -s ${label}-${stage}.tpr -pbc mol -n index.ndx -o ${label}-${stage}-vis.xtc
martiniglass -p ${label}_vis.top -vf
mv vis.vmd ${label}-${stage}-vis.vmd