shahid nayeem wrote:
The attached profile.xvg and histo.xvg are here.
sorry for sending earlier mail without attachments
Shahid Nayeem
On Wed, Mar 7, 2012 at 3:25 PM, shahid nayeem <[email protected]
<mailto:[email protected]>> wrote:
As suggested by you I added some new window and extended some
simulation and I got the attached profile and histo file. Please see
these files. Experimentally it is known that wt protein-protein
interaction is stronger than the mutants. But I get here is reverse.
what could be the possible reason for it. My profile.xvg and
histo.xvg are right or they need more improvement.
I wouldn't base any conclusions off of them. You have a sampling gap at just
over 4 nm in the mutant simulations. More importantly, you do not have a
defined energy minimum in the mutant windows so it is impossible to calculate a
reliable value for DeltaG. Moreover, in the absence of any error estimates, you
can't make any conclusions about these data. g_wham can generate error bars for
you; I'd suggest you do it.
-Justin
Shahid Nayeem
On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul <[email protected]
<mailto:[email protected]>> wrote:
shahid nayeem wrote:
Thanks. But Does that mean that I should look in pullf.xvg
of each window and see whether the value is converged or
not. If not then I should extend the simulation.
I've already made numerous suggestions. The value in pullf.xvg
is a consequence of the nature of the system. Looking at the
interactions between your proteins, the stability of those
proteins, etc. is far more informative, like you would for any
simulation (even those that do not make use of the pull code).
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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