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

[Justin Lemkul]

On 10/16/14 2:51 AM, Batdorj Batsaikhan 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?
>

No.  Stable simulations will not blow up like that.  Moreover, the Gromacs free 
energy code calculates free energy changes as a function of some scaling factor, 
lambda.  You can't just turn on the free energy code and say "this is the free 
energy of my molecule."

-Justin

-- 
==================================================

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

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