[gmx-users] Free energy sampling using G_bar
Justin A. Lemkul
jalemkul at vt.edu
Thu Sep 15 17:21:35 CEST 2011
Fabian Casteblanco wrote:
> Hello all,
> I am finished running a free energy calculation using g_bar and i
> followed Justin Lemkuls tutorial and I am in the process of analyzing
> inorder to determine if I had adequate sampling. I have read the
> 'BAR' paper by Bennett but there are still some concerns whether I
> have enough sampling (see attached). I see in the tutorial that the
> sampling goes up to very large sample numbers, some greater than
> 30,000 where mine only make it to about 300. This 'samples' refers to
Sampling in the tutorial is excessive; I believe I state that in discussing the
free energy output settings.
> how many times a certain energy level was experienced? Does this mean
Yes. The output histograms show the distribution of energy values in
> my system should be left for longer times? My lines don't line as as
> closely as the Methane Decoupling tutorial do. Also, for other
The histograms look fine to me. Lots of overlap.
> solvents that I used, some are giving me a warning for violating the
> 2nd law of thermodynamics and i noticed its because on one of the
> output lines, the entropy decreases a small bit, and some are giving
> me a free energy with a std deviation of at most 1.7 kJ/mol. Does
> this all mean my sampling is not enough?
Perhaps in this instance, yes, but not all of the sampling. You may have to
sample a bit more in the window that's causing problems, but likely not all of
them. I don't know whether uneven sampling (i.e. more points in one window
relative to others) is a problem for BAR.
> Thanks for your help.
> Best regards,
> Fabian F. Casteblanco
> Rutgers University --
> Chemical Engineering PhD Student
> C: +908 917 0723
> E: fabian.casteblanco at gmail.com
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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