[gmx-users] different springs - WHAM

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 15:53:56 CET 2013

On 2/12/13 9:40 AM, Steven Neumann wrote:
> Dear Gmx Users,
> I know it is possible to combine windows with different spring
> constants into the one PMF curve using g_wham.
> Do I have to somehow tell g_wham that one or two windows have
> different spring constants?

No, they are read from the .tpr files.

> For instance - I got the better histogram overlap with lower force
> constant in one window. When I replace this window into the window
> with the sring constant like all windwos (worse overlap) both PMF
> curves differ app. 2kcal/mol which is around 30% of the overall
> deltaG.
> Is there any error I should inroduce when one window differ in terms of k1?

What does g_wham's error analysis suggest?


> The deltaG value of my PMF with all the same windows (springs) is the
> exact experimental value but has worse overlap.
> Can you advise?
> Steven


Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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