Guide developed by: Vaibhav Modi, Aalto University (2021)
This documentation is meant to provide a non-exhaustive collection of guides, tutorials, and other dissemination material for beginners. Gromacs is available to download under the GNU license (https://www.gromacs.org/) and installation instructions are available at https://manual.gromacs.org/documentation/current/install-guide/index.html
INTRODUCTION
Gromacs is a fast and versatile open-source molecular dynamics simulations package. The software is one of the most widely implemented tools for modeling the dynamics of biomolecules at an atomic scale. Gromacs supports the implementation of an array of force fields (AMBER/CHARMM/OPLS/GROMOS) where each force field has its individual advantage based on the type of system.
A brief introduction to Molecular Dynamics simulations (Lecture from BioExcel-2 Summer School 2020)
Tutorials
- MD tutorial - Lysozyme in water (Gromacs 2018)
- MD tutorial - ubiquitin-conjugating enzyme (E2) (Gromacs 4.5.3)
- Introduction to MDP file parameters - video
- File types in Gromacs - link
- Cellulose nanofibril MD tutorial
- Polypropylene matrix MD tutorial
- Building biocomposites
MD Simulation Analysis
There are many sources introducing a different combination of Gromacs tools for trajectory analysis targeting an array of atomistic properties.
Here is a page on the Gromacs server which briefly explains the concept of how each property is computed and an overview for interpretation of the property.
List of output files generated after a simulation run:
- md.log - a log file of simulation run with few key details
- traj.xtc - trajectory file for analysis and visualization
- traj.trr - trajectory with velocities (for restrating runs)
- confout.gro - structure of the system at final time point
- ener.edr - energy file
- state.cpt - checkpoint file with thermostat/barostat
Trajectory visualization
Since Gromacs models the dynamics in a periodic box the system coordinates might be spread across the box in the "xtc" and "trr" files. This will make the visualization very messy but can be fixed quickly with a combination of Gromacs commands:
gmx trjconv -f traj.xtc -s topol.tpr -pbc mol –center –ur compact –o traj-mol.xtc
gmx trjconv –f traj-mol.xtc -s topol.tpr -pbc whole –o traj-mol-vis.xtc
Open Pymol session to visulization the trajectory
load confout.gro, system
load_traj traj-mol-vis.xtc, system
Dissemination material
- A simple flowchart of GROMACS - link (click on individual boxex to understand the role and description of the command)
- A general user guide - link
- Best practice guide - link
- A How-to-guide for different functionalities of Gromacs - link
- Gromacs User Forum - https://gromacs.bioexcel.eu/c/gromacs-user-forum/5
Books
- Good introductory books are: * A. Leach (2001) Molecular Modeling: Principles and Applications. * T. Schlick (2002) Molecular Modeling and Simulation
- With programming background: * D. Rapaport (1996) The Art of Molecular Dynamics Simulation * D. Frenkel, B. Smith (2001) Understanding Molecular Simulation
- More from the physicist’s view: * M. Allen, D. Tildesley (1989) Computer simulation of liquids * H.J.C. Berendsen (2007) Simulating the Physical World: Hierarchical Modeling from Quantum Mechanics to Fluid Dynamics
Using Gromacs on Suhari cluster
After login, load Gromacs and OpenMPI:
module load openmpi/4.0.1-gcc9 gromacs/2020.5
gmx commands can be run interactively in the shell:
gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce
Please send parallel jobs to the queue with jsub:
jsub -np 12 gmx mdrun -s lignocellulose-rf.tpr -maxh 0.25 -resethway -noconfout -nsteps 50 -g logfile