On Feb 14, 2013, at 2:01 PM, Justin Lemkul wrote:
On 2/13/13 5:23 PM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 5:01 PM, Justin Lemkul <[email protected]>
wrote:
On 2/12/13 9:57 AM, Steven Neumann wrote:
On Tue, Feb 12, 2013 at 2:53 PM, Justin Lemkul <[email protected]>
wrote:
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?
-Justin
In both PMF error estimate with bayesian bootstraping is app. 0.2
kcal/mol
Seems like a good result, so what's the problem?
-Justin
That the better overlap of histograms produce worse deltaG comparing
to experiment. With all the same spring constants I get the
experimental value of deltaG but there is a poor overlap. There must
be (somehow) a correction added to deltaG when introdcuing windows
with different spring constants.
The code and/or g_wham paper should address this. In principle,
WHAM can be conducted with any assortment of spring constants you
like. If you track down a bug or something, please report it on
redmine.gromacs.org.
I read (and hacked) g_wham not that long ago. If I recall correctly it
reads the force constants from the tpr. In fact, without those it
would not be able to use pullf files.
A workaround of course would be to simply add another window (or
windows) with the same original force constant that gives adequate
sampling.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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