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

[Lukas Zimmermann]

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
extracted
windows with a spacing of ca 4 degree, and I have simulated each window for
about
2 ns.

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

I get somehow reasonable histograms:

https://www.dropbox.com/s/9mz0gnufdxo1j6r/histo.png?dl=0

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

Lukas