[gmx-users] WHAM with Pull coordinate angle-axis

Lukas Zimmermann luk.zim91 at gmail.com
Sun Aug 28 18:59:27 CEST 2016

Dear GROMACS users,

I used the new Pull Geometry angle-axis to define the angle between a
peptide (with two c-alpha atoms) and the z-axis as pull coordinate. I have
generated a pull trajectory where
this angle changes over time from about 80 degree to 0 degree
approximately, over the
total time of about 1 ns.

I now want to perform Umbrella Sampling along this reaction coordinate and
windows with a spacing of ca 4 degree, and I have simulated each window for
2 ns.

When I use
gmx wham -ix pullx-files.dat -it tpr-files.dat

I get somehow reasonable histograms:


but the profile.xvg file only has NaN in the y column. No further error
messages occur.

Also, if I use -if pullf-files at input, the histograms are plainly wrong,
each just spans about half a degree.

Do you know whether the wham implementation of GROMACS can be used with the
new pull geometries to generate a PMF? Has someone tested this out yet?
Also, which alternative would you suggest for such angle-based PMF? Would
PLUMED be an option?

Thank you very much in advance


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