[gmx-users] problem in energy minimization of protein in lipidmembrane

[Padmani Sandhu]

Hello Justin,


I have solved my problem with energy minimization. Actually box size was
small as compare to the system and some of the periplasmic part was out of
box. After increasing box size in Z-dimension, system get converged easily
to Fmax.


Thank you..!!

Padmani




On Thu, Nov 20, 2014 at 6:34 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

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> On 11/19/14 12:32 PM, Padmani Sandhu wrote:
>
>> Helllo all,
>>
>> I am facing problem with energy minimization of system after reaching
>> desired area per lipid. System is not converging to Fmax < 1000 during
>> final energy minimization. I have turned off all strong position
>> restraints
>> for protein.
>>
>>
> What are the actual values of Fmax and Epot from mdrun?  Note that it also
> prints out the atom bearing Fmax, so that is your first indication of where
> problems may be.  Visualize the output and see what you can learn.
>
> -Justin
>
> --
> ==================================================
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> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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-- 
*Padmani sandhu*
*Research Scholar,*
*Center for Computational Biology and Bioinformatics,*
*Central University of Himachal Pradesh,*
*Temporary Academic Block, Shahpur *
*Pin 176206, District Kangra,*
*Himachal Pradesh, India*