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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
