Web Analytics Made Easy - Statcounter
Skip to content

GROMACS Wizard - Using custom GROMACS version and performance parameters#

This section is part of the GROMACS Wizard tutorial.

Use this page when the default packaged GROMACS setup is not the one you want to run locally.

Before you start#

  • Use this page only for local computations. Cloud jobs ignore the local performance parameters described below.
  • Open GROMACS Wizard first so you can access its Settings button and compare the packaged version with your local installation.
  • If reproducibility matters, decide in advance which exact GROMACS version and force-field directory you want to use.

Using a custom GROMACS version#

GROMACS Wizard comes with one of the latest versions of GROMACS, but it also lets you 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, click the Settings button at the top of GROMACS Wizard.

Open settings

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 browse 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). Custom GROMACS path

Maximum warnings option#

The -maxwarn option can be used to override warnings printed by gmx grompp that otherwise halt execution. In some cases, warnings are harmless, but usually they are not. It is advisable to carefully interpret the output messages before attempting to bypass them with this option. Please note that this is not for normal use and may generate unstable systems.

One of the possible uses is when you simulate a system with a GROMOS force field that leads to a warning; to bypass it, you can set the -maxwarn option to 1.

Note

This option applies both to local and cloud jobs.

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)

Note

These options apply only to local jobs; they are not transmitted to Cloud jobs.

By default, GROMACS Wizard sets the number of threads for local jobs lower than the absolute maximum so that your machine stays responsive while the job is running. If it is set to 0, GROMACS will guess the number of threads automatically. If it is set to a non-zero value below the number of logical cores, GROMACS Wizard also uses -pin on to improve thread placement.

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

Settings

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