As far as I¹ve understood, the absolute distance reported using g_dist (note: alternative name in 5+) and the reported harmonic potential between two groups using pull code in grompp, doesn¹t always match.
As such, I some times end up with neighbouring umbrella histograms practically sitting on top of one another rather than nicely overlapping at the tails. Would anyone with more experience than myself at umbrella sampling clarify whether I should keep in both histograms, or remove one of the hisograms. Also, if my reaction coordinate is an absolute distance and therefor I have set pull_dim = Y Y Y (rather than, say, Z for water through an ion channel or Y for TM protein dimerisation), is it appropriate to use the pullf.xvg and the window.tpr files in g_wham? Or is this beyond the capabilities of g_wham. You see, my reaction coordinate is still distance but it was defined via a traversed trajectory over a potential energy landscape using meta-dynamics. Many thanks Anthony Dr Anthony Nash Department of Chemistry University College London -- 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 [email protected].
