This is a readme file to run molecular dynamics (MD) simulation in GROMACS

• Files in the directory:

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1. PDB file --> 2jof.pdb
2. Directories:

• 1-gmx-input-files # contains script to generate input file
• mdp_files # GROMACS mdp file
• 2-gmx-run # contains scripts to run MD

3. Readme.md file

• Instructions:

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1. check pdb file: use VMD to visualize
2. cd 1-gmx-input-files # enter the directory
3. ./generate-inp-files.sh # execute the script

This will generate the list of files:

• 2jof_box.gro
• 2jof_refined.gro
• 2jof_solv.gro # final simulation box
• posre.itp # protein position restraint file
• topol.top # topology file of the system

4. cd ..
5. cd 2-gmx-run # enter next directory This contains four files:
   Execute the follwing scripts one by one.
   

• sbatch 1-em.sh # Energy minimization

• sbatch 2-eq1.sh # Equilibration first stage

• sbatch 3-eq2.sh # Equilibration second stage

• sbatch 4-prod.sh # Production run

• Running GROMACS tutorial on local mechine:

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• delete all SBATCH commands
• delete module load command
• delete the export command
• change this path /home/apps/gromacs/gromacs-2022.2/installGPUIOMPI/bin/gmx_GPUIMPI to your GROMACS executable path