[gmx-users] Doubt about Free Energy control Minimization

[Justin Lemkul]

On 6/26/17 9:09 AM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I have encountered the following warning when I used the following code to minimize my protein-ligand system when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.
> 
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 
> Warning: 1-4 interaction between 2263 and 2298 at distance 1.004 which is larger than the 1-4 table size 1.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,
> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> 
> 
> I suppose this error is due to setting couple-intramol = no. When it is set to yes, the warning vanishes.
> 
> But, this is my desired setting since, I do not intend to scale the intra molecular interactions even though the ligand is a peptide. Is it reasonable to ignore the warning. If not , how can it affect my resulting structure ? And are all such interaction "ignored for the rest of the simulation" ?
> 

So the system is unstable.  Try minimizing with full interactions before doing 
anything funny with scaling.  And I repeat my caution to you that trying to do 
an alchemical transformation of a peptide is a very unwise choice.  You'll never 
get the simulations to converge in a practical amount of time.

-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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