#!/bin/csh
#

# Generated by CHARMM-GUI (http://www.charmm-gui.org) v3.7

# This folder contains GROMACS formatted CHARMM36 force fields, a pre-optimized PDB structure, and GROMACS inputs.
# All input files were optimized for GROMACS 2019.2 or above, so lower version of GROMACS can cause some errors.
# We adopted the Verlet cut-off scheme for all minimization, equilibration, and production steps because it is 
# faster and more accurate than the group scheme. If you have a trouble with a performance of Verlet scheme while 
# running parallelized simulation, you should check if you are using appropriate command line.
# For MPI parallelizing, we recommand following command:
# mpirun -np $NUM_CPU gmx mdrun -ntomp 1

set init = step5_input
set rest_prefix = step5_input
set mini_prefix = step6.0_minimization
set equi_prefix = step6.%d_equilibration
set prod_prefix = step7_production
set prod_step   = step7


# Minimization
# In the case that there is a problem during minimization using a single precision of GROMACS, please try to use 
# a double precision of GROMACS only for the minimization step.
gmx grompp -f ${mini_prefix}.mdp -o ${mini_prefix}.tpr -c ${init}.gro -r ${rest_prefix}.gro -p topol.top -n index.ndx
gmx_d mdrun -v -deffnm ${mini_prefix}

# Equilibration
set cnt    = 1
set cntmax = 6

while ( ${cnt} <= ${cntmax} )
    @ pcnt = ${cnt} - 1
    set istep = `printf ${equi_prefix} ${cnt}`
    set pstep = `printf ${equi_prefix} ${pcnt}`
    if ( ${cnt} == 1 ) set pstep = ${mini_prefix}

    gmx grompp -f ${istep}.mdp -o ${istep}.tpr -c ${pstep}.gro -r ${rest_prefix}.gro -p topol.top -n index.ndx
    gmx mdrun -v -deffnm ${istep}
    @ cnt += 1
end

# Production
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 ) then
        set pstep = `printf ${equi_prefix} 6`
        gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -p topol.top -n index.ndx
	else
        gmx grompp -f ${prod_prefix}.mdp -o ${istep}.tpr -c ${pstep}.gro -t ${pstep}.cpt -p topol.top -n index.ndx
	endif
    gmx mdrun -v -deffnm ${istep}
    @ cnt += 1
end