#!/bin/bash

FILE=md
TOP=md.top
INCRD=md.incrd
REFC=md.firstcrd

export DO_PARALLEL=""
export BEGIN_PARALLEL=""
export END_PARALLEL=""

/bin/rm -f ${FILE}.out \
           ${FILE}.rst \
           ${FILE}.crd \
           ${FILE}.vel \
           ${FILE}.ene \
           ${FILE}.mdinfo

$BEGIN_PARALLEL
$DO_PARALLEL pmemd.cuda -O -i ${FILE}.in \
        -o ${FILE}.out \
        -p ${TOP} \
        -c ${INCRD} \
        -r ${FILE}.rst \
        -x ${FILE}.nc  \
        -v ${FILE}.vel \
        -e ${FILE}.ene \
        -ref ${REFC} \
        -inf ${FILE}.mdinfo
$END_PARALLEL

