Plot profile.xvg

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Hi, I am new to GROMACS and MD in general.

I just got the file “profile.xvg” after running umbrella sampling for my protein-protein complex.
How do I obtain the resulting PMF and corresponding umbrella histograms?

xmgrace does not work on my mac for some reason. I used excel to plot “profile.xvg” but it looks nothing like the turorial.

Can anyone help me with this?

Thank you

2

Hi,
You can use gmx wham gmx wham — GROMACS 2022.3 documentation to compute a potential of mean force from umbrella sampling output.

You can also have a look at the umbrella sampling tutorial for some explanation and help
https://tutorials.gromacs.org/umbrella-sampling.htm.

\Alessandra