GROMACS-recipes is an unofficial collection of instructions for using the molecular dynamics (MD) simulation package GROMACS. The goal is to collect validated protocols for setting up and running the various kinds of MD simulations offered by the software. The contents of this repository are not intended to serve as an introduction to GROMACS or to MD simulations in general.
Unless stated otherwise, GROMACS versions 2020.3 and 2021.1 are used throughout the examples provided, although the protocols should work with other reasonably recent versions of the software as well.
If performance is of any concern to you, consider building GROMACS from source. Follow the installation guide to understand your options and select the most appropriate settings for your machine. The options I usually pass to cmake are
-DCMAKE_C_COMPILER=/usr/bin/gcc-8 \
-DCMAKE_CXX_COMPILER=/usr/bin/g++-8 \
-DCMAKE_INSTALL_PREFIX=/home/david/Programs/gromacs-2020.3 \
-DGMX_BUILD_OWN_FFTW=ON \
-DGMX_GPU=ON \
-DREGRESSIONTEST_DOWNLOAD=ON
for GROMACS 2020.3, and
-DCMAKE_C_COMPILER=/usr/bin/gcc-8 \
-DCMAKE_CXX_COMPILER=/usr/bin/g++-8 \
-DCMAKE_INSTALL_PREFIX=/home/david/Programs/gromacs-2021.1 \
-DGMX_BUILD_OWN_FFTW=ON \
-DGMX_GPU=CUDA \
-DGMXAPI=OFF \
-DREGRESSIONTEST_DOWNLOAD=ON
for GROMACS 2021.1. Check the output of cmake carefully and make adjustments if needed. Don't forget to run the tests after building the software.
The force fields (FFs) bundled with GROMACS are quite ancient. If comparison with previous works (utilizing these FFs) is not your primary goal, more recent FFs should be downloaded, installed, and used. Good choices include the CHARMM36 or the ff14SB/OL15 FFs; other FFs are available as volunteer contributions on the GROMACS website.
Instructions for running various kinds of MD simulations can be found in protocols/. Protocol names have the form version_FF_system[_modification], where version is the GROMACS version used, FF is the name of the FF used, system is the type of biological system simulated (e.g., protein, DNA, lipid, ...), and modification is an optional alteration of the base protocol (for the given GROMACS version, FF, and system type). It is expected that the required FF files are installed on the system when using the respective protocols.