On 7/8/13 4:27 PM, mike.ne...@stud.uni-due.de wrote:
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?
Perhaps I'm a bit confused on how you're presenting the question. Are you
asking about "forward" and "reverse" transformations giving an equivalent
result? Keep in mind that there is no such directionality in these types of
transformations, as long as you're not using a slow-growth method. Otherwise, I
don't see how one can have left-handed overlap but not right-handed overlap in
adjacent distributions. Either the neighboring lambda windows overlap or don't.
So, concluding this, the last two cases should be right, but refering to the
"mailing-list-question" of Fabian Casteblanco
http://gromacs.5086.x6.nabble.com/Free-energy-sampling-using-G-bar-td4455419.html#a4455420
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?
The list does not accept attachments. Please provide a URL to share the file.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Postdoctoral Associate
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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