GROMACS version: 2020.3
GROMACS modification: No
Here post your question:
I was wondering how one can generate the curves for histograms after getting the histo.xvg, something such as what Justin Lemkul did on his Umbrella Sampling tutorial.
Is there any systematic approach or software that we can use?
Kind regards,
ES.
xmgrace -nxy histo.xvg
I would like to kindly ask a related question. In the recently published version of GROMACS tutorials:
https://pubs.acs.org/doi/full/10.1021/acs.jpcb.4c04901
there PMF profile was calculated together with error bars.
What command / xmgrace options should I use to obtain a plot similar to that obtained in the tutorial:
in order to obtain a shaded “uncertainty corridor” and not single error bars?
Are you asking where the error estimates come from or simply how to plot them? For the former, gmx wham has a built-in bootstrap sampling algorithm. For the latter, you’re probably better off using Python (matplotlib) for plotting rather than xmgrace, where it should be relatively easy to achieve (e.g. by plotting a shaded region using plt.fill_between() to draw the shaded error region).