[gmx-users] pmf contradicts <E_pot>

alexander yakovenko yakovenko_a at ukr.net
Thu Jan 26 02:37:27 CET 2012

Dear colleagues,


I have a problem with PMF calculations with umbrella sampling. A small
part of a big molecule migrates from conformation A to conformation B.
Although g_wham computes free energy as positive value of ~70kJ/mol for
A->B transformation, an average potential energy of the fragment
decreases along the trajectory. So in window that corresponds to state A
it is -2292kJ/mol and in window corresponding to state B it is -2379
kJ/mol (and the loss looks roughly linear between A and B). The question
is follows: how a sampling along a trajectory of decreasing potential
energy can yield positive pmf and vice versa? Are there any ideas of what
goes wrong in my simulations?


P.S. It was a protein molecule simulated with GROMOS96 FF in spc water
box and umbrella sampling was of 12 ns per window.

Post Doctoral Fellow
Genome Sciences Centre
Vancouver, BC
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