[gmx-users] Umbrella_pull_simulation

[Justin A. Lemkul]

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 <msnayeem at gmail.com 
> <mailto:msnayeem at gmail.com>> 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 <jalemkul at vt.edu
>     <mailto: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
>         MILES-IGERT Trainee
>         Department of Biochemistry
>         Virginia Tech
>         Blacksburg, VA
>         jalemkul[at]vt.edu <http://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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-- 
========================================

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

========================================