[gmx-users] Which/What is the adequate overlap using g_BAR

mike.nemec at stud.uni-due.de mike.nemec at stud.uni-due.de
Mon Jul 8 22:27:21 CEST 2013

Dear Gromacs People,

I want to calculate free energy differences between two states A and B
using g_BAR.

For this I read many papers concerning the overlap between neighboring
sample windows (Delta H) but I am still wondering about the following issue:

I know, that there has to be an adequate overlap to get accurate free
energy differences, but I am not sure, which neighboring sample
distributions have to overlap in the gromacs nomenclature.

Do the neighboring distributions N(Delta H(lambda=0.05) | lambda=0) AND
N(Delta H(lambda=0) | lambda=0.05) have to overlap? Or shall there be an
overlap between neighboring distributions calculated from the left side

N(Delta H(lambda=0.05) | lambda=0) ; N(Delta H(lambda=0.10) |
lambda=0.05) ; N(Delta H(lambda=0.15) | lambda=0.10) ...

and then neighboring from the right side

N(Delta H(lambda=0) | lambda=0.05) ; N(Delta H(lambda=0.05) |
lambda=0.10) ; N(Delta H(lambda=0.10) | lambda=0.15) ... ?

I am puzzled, because if one takes a hypothetic stepsize of "1", then
one only gets two distributions

N(Delta H(lambda=1) | lambda=0) AND N(Delta H(lambda=0) | lambda=1)

which then should overlap to get a right free energy difference
estimation. Am I right?
So, concluding this, the last two cases should be right, but refering to the
"mailing-list-question" of Fabian Casteblanco
Justin Lemkul replies, that "the histograms look fine [...]. Lots of
overlap.", which would result, that all the "left-side" and all the
"right-side" neighbor distributions have to overlap, I think

Depending on your answer, can you please explain, why thedistributions
of your answer have to overlap, and not the others?

For this case I calculated the free energy difference with g_BAR of one
tripeptide Valine-Leucine-Valine where thepartial charges of the Leucine
are turned to "0" from state A to B in steps of "0.02" (see attachement,
representative 4 neighboring distributions). In the case, that all the
"left side calculated" and all the "right side calculated" neighbor
distributions have to overlap, the overlap in the attached file is great,
isn't it?
But is that really the correct overlap?

Thank you in advance,

Mike Nemec

More information about the gromacs.org_gmx-users mailing list