[gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 6/29/17 5:11 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I am getting the same following warning even after minimizing the system twice using cg integrator. This is only when the free energy stuff is inserted in the energy minimization code.
> 
> " WARNING: Listed nonbonded interaction between particles 2263 and 2298 at distance 3f which is larger than the table limit 3f 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. "
> 
> 
> When the system is minimized without free energy code, it shows no warning. Hence, I suppose it is due to the free energy code itself with couple-intramol = no.
> 
> I found the warning disappears when couple-intramol = yes. But this is not I would like to do, since intra molecular interactions need not be scaled/perturbed.
> 
> It's definitely true that the "listed interaction inside a smaller molecule you are decoupling during a free energy calculation".
> 
> When the table-extension is increased to 4 nm with couple-intramol = no, the warning again disappears. Should I go forward with this setting and how will it affect the energy minimization of my system?
> 

Increasing the table-extension means mdrun will permit distorted structures that 
may be totally unreasonable.  It is generally unwise to increase it, and 
especially if you're increasing it that much.

-Justin

-- 
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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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