A molecular dynamics workflow can look identical from one run to the next while quietly using different software or force-field files. That matters when you are trying to reproduce a result, compare calculations across machines, or troubleshoot why a local run behaves differently from an expected setup.
In SAMSON’s GROMACS Wizard, you can select a locally installed GROMACS version instead of using the version packaged with the extension. The important detail is that choosing the executable is only part of the setup: you also need to point the wizard to the folder containing the force fields. Treat these as a pair, and verify both before launching a calculation.
Make the software choice explicit
Open the GROMACS Wizard and select Settings. The panel shows the version of the packaged GROMACS installation. To use a different local installation, enable Use a different GROMACS version, then browse to the executable: gmx.exe on Windows, or gmx on Linux and macOS.
The wizard displays the detected version when it recognizes the executable. If it displays invalid, pause before proceeding: the selected file has not been recognized as a valid GROMACS executable. Check that you chose the executable itself and that it belongs to the installation you intend to use.
Do not forget the force-field directory
Next, choose the force-fields folder—the directory containing the forcefield.ff folders. For example, on Linux or macOS, it may be located at $HOME/gromacs/share/top/. The location depends on your installation, so use the folder that belongs to the GROMACS setup you selected rather than assuming every installation uses the same path.
Why does this second path matter? A correct executable does not, by itself, tell the wizard where to find the force-field files needed for a calculation. Before running, check that the executable and force-field directory are both from the intended installation. This simple pairing is especially useful when multiple GROMACS versions are installed on one machine or when a project requires a specific version for reproducibility.
Know which settings affect which jobs
There is an important distinction between software selection, performance tuning, and warning handling:
- Custom GROMACS version: select the local executable and its force-field directory for local computations.
- Performance parameters: options such as
ntmpi,ntomp,pme, andmaxhapply to local jobs. They are not transmitted to Cloud jobs. - Maximum warnings:
-maxwarnapplies to both local and Cloud jobs.
For local performance, GROMACS Wizard sets the thread count below the machine’s absolute maximum by default, helping keep the computer responsive while a job runs. A value of 0 lets GROMACS choose the thread count automatically. If you specify a non-zero number below the logical-core count, the wizard also uses -pin on to improve thread placement. These controls can be useful when balancing simulation speed with the ability to keep working on the same computer.
GROMACS already has mechanisms to detect hardware and use it effectively, so changing performance parameters is not automatically an improvement. If you do tune them, change settings deliberately and keep a record of what you changed. That makes it easier to understand performance differences between runs.
Treat warnings with care
The -maxwarn option can let gmx grompp continue despite warnings that would otherwise halt execution. Some warnings may be harmless in a particular context, but warnings can also indicate a problem, and bypassing them may produce an unstable system. Read and interpret the messages before increasing the allowed warning count. One documented example is a GROMOS force-field warning that may be bypassed by setting -maxwarn to 1; this is a specific case, not a general recommendation to ignore warnings.
Once the paths and settings are checked, return to the calculation you want to run locally and launch it. For the full instructions, see the GROMACS Wizard settings documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.