[gmx-users] distance issues with umbrella sampling

Nash, Anthony a.nash at ucl.ac.uk
Wed Aug 19 16:54:15 CEST 2015

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

Dr Anthony Nash
Department of Chemistry
University College London

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