#!/bin/bash

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

# This folder contains GROMACS formatted 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 recommend following command:
# mpirun -np $NUM_CPU gmx mdrun -ntomp 1

init="step5_input"
rest_prefix="step5_input"
mini_prefix="step6.0_minimization"
equi_prefix="step6.%d_equilibration"
prod_prefix="step7_production"
prod_step="step7"
awh_prefix="step8_awh"

# 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 -maxwarn 5
gmx mdrun -v -deffnm "${mini_prefix}"

if [ -f "${mini_prefix}.tpr" ]; then
    echo "${mini_prefix}.tpr already exists, skipping grompp for minimization"
else
   /usr/local/gromacs/avx_512/bin/gmx grompp -f "${mini_prefix}.mdp" -o "${mini_prefix}.tpr" -c "${init}.gro" -r "${rest_prefix}.gro" -p "${topol}" -n "${index}" -maxwarn 5
fi

if [ -f "${mini_prefix}.gro" ]; then
    echo "${mini_prefix}.gro already exists, skipping mdrun for minimization"
else
   gmx mdrun -v -deffnm "${mini_prefix}"
fi

# Equilibration
cnt=1
cntmax=6

while [ "$cnt" -le "$cntmax" ]; do
    pcnt=$((cnt - 1))
    istep=$(printf "${equi_prefix}" "$cnt")
    pstep=$(printf "${equi_prefix}" "$pcnt")

    if [ "$cnt" -eq 1 ]; then
        pstep="${mini_prefix}"
    fi

    # Prüfen, ob die TPR-Datei schon existiert
    if [ -f "${istep}.tpr" ]; then
        echo "${istep}.tpr exists, skipping to the next step."
        cnt=$((cnt + 1))
        continue
    fi

   gmx grompp -f "${istep}.mdp" -o "${istep}.tpr" -c "${pstep}.gro" -r "${rest_prefix}.gro" -p topol.top -n index.ndx -maxwarn 5

    # Prüfen, ob die Simulationsergebnis-Datei schon existiert
    if [ -f "${istep}.gro" ]; then
        echo "${istep}.gro exists, skipping mdrun."
    else
        gmx mdrun -v -deffnm "${istep}"
    fi

    cnt=$((cnt + 1))
done

# Production (step 7)
#cnt=1
#cntmax=2

#while [ "$cnt" -le "$cntmax" ]; do
#    pcnt=$((cnt - 1))
#    istep="${prod_step}_${cnt}"
#    pstep="${prod_step}_${pcnt}"

    # Prüfen, ob die TPR-Datei schon existiert
#    if [ -f "${istep}.tpr" ]; then
 #       echo "${istep}.tpr exists, skipping to the next step."
 #       cnt=$((cnt + 1))
 #       continue
  #  fi

  #  if [ "$cnt" -eq 1 ]; then
   #     pstep=$(printf "${equi_prefix}" 6)
   #     gmx grompp -f "${prod_prefix}.mdp" -o "${istep}.tpr" -c "${pstep}.gro" -p topol.top -n index.ndx -maxwarn 5
   # else
   #     gmx_mpi grompp -f "${prod_prefix}.mdp" -o "${istep}.tpr" -c "${pstep}.gro" -t "${pstep}.cpt" -p topol.top -n index.ndx -maxwarn 5
 #   fi

    # Prüfen, ob die Simulationsergebnis-Datei schon existiert
   # if [ -f "${istep}.gro" ]; then
   #     echo "${istep}.gro exists, skipping mdrun."
  #  else
   #     gmx mdrun -v -deffnm "${istep}"
   # fi

   # cnt=$((cnt + 1))
#done

# AWH Production (step 8)

    gmx grompp -f step8_awh.mdp -o step8_awh.tpr -c step6.6_equilibration.gro -p topol.top -n index.ndx -maxwarn 5

    gmx mdrun -deffnm step8_awh

    gmx awh -more -f step6.6_equilibration.edr  -s step6.6_equilibration.tpr
#done