[gmx-users] Umbrella_pull_simulation

[shahid nayeem]

The similar files for wt can be assesed at
 http://www.freefilehosting.net/umbrellawt
 I expected wild type binding energy to be less than mutant
The command used for g_wham is
 g_wham_mpi_4.5.4  -it tpr-files.dat -if pullf-files.dat -o profile_mut.xvg
-hist histo_mut.xvg -unit kCal -b 500 -nBootstrap 200 -bsres
bsResult_mut.xvg -bsprof bsprofile_mut.xvg  -ac
I get the values exactly opposite to my expectation and unable to find out
where I am wrong please suggest.
Shahid Nayeem

On Thu, Mar 15, 2012 at 3:31 PM, shahid nayeem <msnayeem at gmail.com> wrote:

> 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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