Klauda Lab Simulation Wiki

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==== GROMACs Simulations ====

This is based on taking CHARMM-GUI input files and adjusting these for use on Zaratan.

**1. Create a Minimization and Equilibration File**

The code below provides an example setup for this.

<code commend>
#!/bin/bash
#SBATCH --job-name=eq_bilayer
#SBATCH -A energybio-eng
#SBATCH -t 72:00:00
#SBATCH -N 1
#SBATCH -n 32

module load gromacs/2019.4/gcc/
export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
set -euo pipefail

# ---- 6.0 Minimization ----
#srun gmx_mpi grompp -f step6.0_minimization.mdp \
 # -c step5_input.gro -r step5_input.gro -p topol.top -n index.ndx \
  #-o step6.0_minimization.tpr
#srun gmx_mpi mdrun -deffnm step6.0_minimization

# ---- 6.1 Equilibration ----
#srun gmx_mpi grompp -f step6.1_equilibration.mdp \
  #-c step6.0_minimization.gro -r step5_input.gro -p topol.top -n index.ndx \
  #-o step6.1_equilibration.tpr
#srun gmx_mpi mdrun -deffnm step6.1_equilibration

# ---- 6.2 ----
srun gmx_mpi grompp -f step6.2_equilibration.mdp \
  -c step6.1_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx \
  -o step6.2_equilibration.tpr
srun gmx_mpi mdrun -deffnm step6.2_equilibration

# ---- 6.3 ----
srun gmx_mpi grompp -f step6.3_equilibration.mdp \
  -c step6.2_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx \
  -o step6.3_equilibration.tpr
srun gmx_mpi mdrun -deffnm step6.3_equilibration

# ---- 6.4 ----
srun gmx_mpi grompp -f step6.4_equilibration.mdp \
  -c step6.3_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx \
  -o step6.4_equilibration.tpr
srun gmx_mpi mdrun -deffnm step6.4_equilibration

# ---- 6.5 ----
srun gmx_mpi grompp -f step6.5_equilibration.mdp \
  -c step6.4_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx \
  -o step6.5_equilibration.tpr
srun gmx_mpi mdrun -deffnm step6.5_equilibration

# ---- 6.6 ----
srun gmx_mpi grompp -f step6.6_equilibration.mdp \
  -c step6.5_equilibration.gro -r step5_input.gro -p topol.top -n index.ndx \
  -o step6.6_equilibration.tpr
srun gmx_mpi mdrun -deffnm step6.6_equilibration
</code>

**2. Run the minimization and equilibration files**

Using the created SBATCH file above, submit this to the queue to run the simulation

If there are errors in running the equilibration files, it is possible to run a single step alone, for example, step6.2_equilibration as shown below. This is only needed if the steps . 

<code commend>
#!/bin/bash
#SBATCH --job-name=eq_nic
#SBATCH -A energybio-eng
#SBATCH -t 72:00:00
#SBATCH -n 1
#SBATCH -N 1

module load gromacs/2019.4/gcc/

#equilibration

mpirun gmx_mpi grompp -f step6.2_equilibration.mdp -o step6.2_equilibration.tpr -$

# Run the equilibration 
mpirun gmx_mpi mdrun -deffnm step6.2_equilibration
</code>

**3. Create an initial production run SBATCH file**

<code commend> 
#!/usr/bin/env bash
#SBATCH --job-name=orf7b-alesnic
#SBATCH --qos=normal
#SBATCH --account=energybio-eng
#SBATCH --partition=standard
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=64G
#SBATCH --time=24:00:00

module purge
module load gromacs/2019.4/gcc/
module list

export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK}"

# Production run
srun gmx_mpi grompp -f step7_production.mdp \
  -c step6.6_equilibration.gro -p system.top -n index.ndx \
  -o step7_production.tpr

srun gmx_mpi mdrun -deffnm step7_production
</code>


**4. Create a second production run file to finish the simulation**

Note: This is assuming the simulation can finish with desired # of steps (-until flag). If not, you will need to create additional restart files to continue until the time has reached.

<code commend>
#!/usr/bin/env bash
#SBATCH --job-name=orf7b-ancont
#SBATCH --qos=normal
#SBATCH --account=energybio-eng
#SBATCH --partition=standard
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=32
#SBATCH --mem=64G
#SBATCH --time=24:00:00

module purge
module load gromacs/2019.4/gcc/
module list
export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK}"

#extend just makes the total sim time longer. Use --until to stop exactly at 10us
gmx_mpi convert-tpr -s step7_production.tpr -until 10000000 -o step7_production_extended.tpr

srun -n ${SLURM_NTASKS} gmx_mpi mdrun \
  -s step7_production_extended.tpr \
  -deffnm step7_production_extend \
  -cpi step7_production.cpt \
  -noappend \
  -pin on -dlb auto -ntomp ${SLURM_CPUS_PER_TASK} \
  -cpt 10 -resethway -v
</code>