Colvar module with GROMACS does not work

User discussions
1

GROMACS version: 2022.5
GROMACS modification: No
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Dear GROMACS community,

I need to perform umbrella sampling simulations. For generation of the umbrella sampling windows, I would like to use the “colvars” module, which, according to the documentation (https://colvars.github.io/master/colvars-refman-gromacs.pdf)), can be used in gromacs.

Following the procedures described in this manual, I launch the following command:

gmx mdrun -s prod_Q1M_pull_008.tpr -deffnm md -colvars distPull.dat

where “distPull.dat” is the file specifying the collective variables.

However, the command above shows “invalid command line options”.

Can you please let me know how can I properly launch the “colvar” module? Does it need to be manually activated, in order to make it work?

Your help will be much appreciated.

Best regards,
Oleksii

2

The colvars module will be enabled in the GROMACS 2024 release. The 2024-beta will be released very soon.

3

Hi alzdorev,

For GROMACS 2022 version, you need to patch the GROMACS source files to activate the colvars module.
We (the colvars team) provide already patched source files for 2022 at this link : Tags · Colvars/gromacs · GitHub.
Then you need to compile the files and the -colvars command line options will be available.

As @MagnusL said, colvars will be shipped by default for the 2024 release and the above procedure won’t be necessary anymore.

4

Hi @MagnusL and @Hub,

Thanks a lot for your help. I see the new version of GROMACS has already been released. Will now try it out.