GROMACS

A versatile package for performing molecular dynamics simulations and energy minimization.

Overview

GROMACS is a powerful molecular dynamics simulation package widely used in computational chemistry and biophysics. It offers high performance, flexibility, and a rich set of analysis tools.

Features

High-performance molecular dynamics simulations
Energy minimization
Free energy calculations
Extensive analysis tools
GPU acceleration support

Installation

Requirements

C++ compiler (GCC 7.0+)
CMake 3.10+
MPI library (optional)
CUDA toolkit (for GPU support)

Installation Steps

Download the source code:

wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-2021.3.tar.gz
tar xvf gromacs-2021.3.tar.gz
cd gromacs-2021.3

Configure and compile:

mkdir build
cd build
cmake .. -DGMX_BUILD_OWN_FFTW=ON
make -j 4
sudo make install

Basic Usage

Preparing Input Files

Prepare protein structure file (PDB format)

Generate topology file:

gmx pdb2gmx -f protein.pdb -o processed.gro -water spce

Define simulation box:

gmx editconf -f processed.gro -o newbox.gro -c -d 1.0 -bt cubic

Add solvent:

gmx solvate -cp newbox.gro -cs spc216.gro -o solv.gro -p topol.top

Energy Minimization

Prepare energy minimization parameters

Run energy minimization:

gmx grompp -f em.mdp -c solv.gro -p topol.top -o em.tpr
gmx mdrun -v -deffnm em

Molecular Dynamics Simulation

Prepare MD parameters

Run MD simulation:

gmx grompp -f md.mdp -c em.gro -p topol.top -o md.tpr
gmx mdrun -v -deffnm md

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