[gmx-users] Umbrella_pull_simulation

shahid nayeem msnayeem at gmail.com
Wed Mar 7 10:55:24 CET 2012

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
Shahid Nayeem

On Tue, Feb 28, 2012 at 7:44 PM, Justin A. Lemkul <jalemkul at vt.edu> 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
> Department of Biochemistry
> Virginia Tech
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> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> ==============================**==========
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