What is the currently best OS for GROMACS?

User discussions
1

GROMACS version:
GROMACS modification: Yes/No
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This might be a very dumb question: I know that GROMACS should be run in a Linux environment, but can I install a Linux subsystem under Windows?

Also, is Ubantu the recommonded Linux OS for GROMACS? If so, what is the currently most “mature” version of Ubantu?

Thanks in advance.

2

WSL is not as fast as native Linux. That’s because WSL couldn’t really efficiently utilise the CUDA cores on GPU. If you want to run a CPU-only simulation that would not be significantly different from native Linux.

Ubuntu is good. I am still using a 4+ years old LTS edition and it works fine. I suggest that you look at the latest LTS version that’s available. But mind it that the latest versions may have more recent compilers that may not be compatible with certain stuff.

3

Thanks for your suggestion. I have used a native Ubuntu 24.04.3 LTS and it works fine.

I installed Gromacs 2025.3 following the Quick and dirty installation on the GROMACS website, but the gmx -version command shows “GPU support: disabled”. Do I need to uninstall the existing Gromacs to do a complete installation?

4

Did you install a compatible CUDA toolkit version before installing Gromacs? Check this with nvidia-smi command.

A word of caution here: do check compatibility of compliers with Gromacs and CUDA as well as Cmake.

5

Thanks. nvidia-smi command gives the following result:

±----------------------------------------------------------------------------------------+
| NVIDIA-SMI 580.65.06 Driver Version: 580.65.06 CUDA Version: 13.0 |
±----------------------------------------±-----------------------±---------------------+
| GPU Name Persistence-M | Bus-Id Disp.A | Volatile Uncorr. ECC |
| Fan Temp Perf Pwr:Usage/Cap | Memory-Usage | GPU-Util Compute M. |
| | | MIG M. |
|=========================================+========================+======================|
| 0 NVIDIA GeForce RTX 5090 Off | 00000000:01:00.0 On | N/A |
| 0% 25C P8 23W / 575W | 429MiB / 32607MiB | 1% Default |
| | | N/A |
±----------------------------------------±-----------------------±---------------------+

±----------------------------------------------------------------------------------------+
| Processes: |
| GPU GI CI PID Type Process name GPU Memory |
| ID ID Usage |
|=========================================================================================|
| 0 N/A N/A 2685 G /usr/lib/xorg/Xorg 115MiB |
| 0 N/A N/A 2896 G /usr/bin/gnome-shell 36MiB |
| 0 N/A N/A 5612 G …/7177/usr/lib/firefox/firefox 220MiB |
±----------------------------------------------------------------------------------------+

I probably did not install CUDA toolkit.

6

The quick and dirty installation does not install CUDA support. To enable this, you need to enable it via a cmake option, e.g. -DGMX_GPU=CUDA -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda. For more details, see this section of the install guide.

If you only want one version of GROMACS on your workstation, no need to delete an existing version, it will simply be overwritten. If you want more than one version (e.g. one with GPU support and one without), consider setting -DCMAKE_INSTALL_PREFIX to different paths.

7

Thanks a lot. I will give it a try.