[gmx-users] Umbrella_pull_simulation

[shahid nayeem]

I have added some new windows in mutant umbrella sampling which removes the
sampling gap around 4 nm. Also I sampled more windows in the initial COM
distance in the hope that I get energy minimum of profile well defined. I
also did boot strapping for error estimates. The files can be assessed at
http://www.freefilehosting.net/umbrellamut


On Wed, Mar 7, 2012 at 4:38 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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://vt.edu/Pages/Personal/justin>
>>        <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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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