[gmx-users] some thoughts on gmx wham

[Alex]

This is probably for Justin once again...
My understanding is that you plan to work on a new tutorial for PMF
calculations, so may be this could be useful. I recall asking you about
selection of k and the corresponding spacing between configurations. We
agreed that there is no strict way of setting this up to achieve decent
overlapping between histograms. And I've been having a pretty hard time
getting proper convergence while guessing e.g. spacing.

For "heavy" objects this problem remains, but for e.g. ions it seems there
is a way to get a semi-quantitative handle, which helped me quite a bit.
For a given reaction coordinate, the position "spread" is of order x =
sqrt(k_boltz*T/k), where k is the bias spring constant, i.e. this is the
order of position's sigma. What worked for me is spacing between configs
equal to x. For example, with k = 1000 kJ/mol/nm2, T = 300 K, we get x =
0.5 A, and with spacing close to x, we get good convergence. Prior to that,
I used spacing of 1 A and would sometimes get "gaps" in the PMF curve after
wham's attempts to converge for something like half a million iterations.

Alex