RAU_MasterStudy/thesis/old/openmm_help

#!/bin/csh
#

# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.7
#
# This folder contains a pre-optimized PDB structure and OpenMM inputs.
# All input files were optimized for OpenMM v6.2 or above, so lower version of OpenMM can cause some errors.
# You can get the latest development version of OpenMM at the git repository:
# https://github.com/pandegroup/openmm

set init = step4_input
set equi_prefix = step5_equilibration
set prod_prefix = step6_production
set prod_step   = step6

# Equilibration
set input_param = "-t toppar.str -p ${init}.psf -c ${init}.crd -b sysinfo.dat"
python -u openmm_run.py -i ${equi_prefix}.inp ${input_param} -orst ${equi_prefix}.rst -odcd ${equi_prefix}.dcd > ${equi_prefix}.out

# Production
# The OpenMM check point file (.chk) cannot be used in a different machine environment.
# So please make sure if you are using the same GPU and CUDA version of machine while doing additional
# production steps with the check point file.
set cnt = 1
set cntmax = 10

while ( ${cnt} <= ${cntmax} )
    @ pcnt = ${cnt} - 1
    set istep = ${prod_step}_${cnt}
    set pstep = ${prod_step}_${pcnt}
    if ( ${cnt} == 1 ) set pstep = ${equi_prefix}
    set input_param = "-t toppar.str -p ${init}.psf -c ${init}.crd -irst ${pstep}.rst"
    python -u openmm_run.py -i ${prod_prefix}.inp ${input_param} -orst ${istep}.rst -odcd ${istep}.dcd > ${istep}.out
    @ cnt += 1
end