GROMACS Wizard – Using custom GROMACS version and performance parameters

This section is a part of the GROMACS Wizard tutorial.

Using a custom GROMACS version

GROMACS Wizard comes with one of the latest versions of GROMACS. But it also provides you with the possibility to use your own version of GROMACS for local computations. This might be useful if you would like to use the GROMACS package installed on your system or use a specific GROMACS version for reproducibility reasons.

To use a locally installed version of GROMACS, press the Settings button () at the top of GROMACS Wizard. There you can see the version of the shipped GROMACS package. If you would like to use another version of GROMACS that is installed on your machine, then check the Use a different GROMACS version option and provide two paths:

  1. A path to the GROMACS executable (gmx.exe on Windows or gmx for Linux and MacOS) by clicking on the button . Note that the version of the chosen GROMACS package will also be displayed (if the executable was not recognized then “invalid” will be displayed instead).
  2. A path to the force fields folder where all the forcefield.ff folders are present (e.g. $HOME/gromacs/share/top/ on Linux and MacOS).

Additional performance parameters

“The GROMACS build system and the gmx mdrun tool have a lot of built-in and configurable intelligence to detect your hardware and make pretty effective use of it. For a lot of casual and serious use of gmx mdrun, the automatic machinery works well enough.” (source: GROMACS Manual)

The Settings provide you with the possibility to specify additional performance parameters which will be used when running GROMACS locally. For example, you can specify the level of parallelization, control parameters of domain decomposition, and PME algorithms.

The possible options include but are not limited to, for example: nt, ntmpi, ntomp, pme.
Please see the link following for more information and more options: GROMACS Manual – Getting good performance from mdrun.

Comments are closed.