This repository is particularly for the documentation of 2021 APAC HPC-AI Competition, specifically for group MAAZICKS.

High-Performance Computing – GROMACS (GROningen MAchine for Chemical Simulations)

• Explain how Gromacs was configured, compiled and deployed Makefile
• Showcase the ways on running the MD
• Optimise the performance (ns/day) and wall time (s)

• portable binary run input file that contains the starting structure of your simulation, the molecular topology and all the simulation parameters.

• GROMACS

  Note: To check the package in server (linux-based)
  

  module avail
  

Step 1: Load GROMACS
module load {gromacs-package-PATH}

Step 2: Run MD
mpirun -np {number of processors available} mdrun_mpi -s {input file} -v -noconfout -resethway -nsteps {number of steps} -ntomp {number of omp threads} -gcom {numbers before communcation phases} -nstlist {numbers before list converging}

Please refer to the HPC-GROMACS folder.

Li Chuin Chong (Team Lead), Bezmialem Vakıf Universty
Jeremias Ivan, Indonesia International Institute for Life Sciences
Muhammad Zainul Arifin Nasution, Indonesia International Institute for Life Sciences
Stefanus Bernard, Indonesia International Institute for Life Sciences
Aakib Bin Nesar, North South University Bangladesh
Eo Yeo Keat, University Putra Malaysia

Kenneth Ban Hon Kim (Advisor), National University of Singapore
Ayesha Fatima (Advisor), Bezmialem Vakıf Universty