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gromacs

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gromacs [2025/10/24 09:35] – created admingromacs [2025/10/24 09:47] (current) – admin
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 The code below provides an example setup for this. 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>
gromacs.1761312957.txt.gz · Last modified: 2025/10/24 09:35 by admin