[gmx-users] How long run should be enough for Free Energy Calculation of a protein?

[Batdorj Batsaikhan]

Dear gmx user,

please give me advice about above calculations. Thanks.


Batsaikhan




On Thursday, October 16, 2014 2:51 PM, Batdorj Batsaikhan <batsaikhanbat at yahoo.com> wrote:
 


I want to calculate free energy of 2 different types of 71 amino acids long protein.

I run General Equilibration (NPT). Then I run free energy calculation of 200 ps. 

When calculation start, I got following warming message: 

**********************************
WARNING: Listed nonbonded interaction between particles 27 and 159
at distance 2.056 which is larger than the table limit 2.029 nm.

This is likely either a 1,4 interaction, or a listed interaction inside
a smaller
 molecule you are decoupling during a free energy calculation.
Since interactions at distances beyond the table cannot be computed,
they are skipped until they are inside the table limit again. You will
only see this message once, even if it occurs for several interactions.

IMPORTANT: This should not happen in a stable simulation, so there is
probably something wrong with your system. Only change the table-extension
distance in the mdp file if you are really sure that is the reason.
***********************************

Question: Is these calculation reliable? 


Best regards,

Batsaikhan




On Wednesday, October 15, 2014 7:34 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
 





On 10/14/14 11:37 PM, Batdorj Batsaikhan wrote:
> Dear gmx-users,
>
> Hello, I am working on free energy calculation of a protein. How long run should be enough for Free Energy Calculation of a protein?
>

How is it that you're attempting to calculate this quantity?

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
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Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul


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