[gmx-users] Doubt about Free Energy control Minimization

[Varvdekar Bhagyesh Rajendra]

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" ?

Apologies for the previous incomplete mail.

Best Regards,

Bhagyesh

----- Original Message -----
From: "Justin Lemkul" <jalemkul at vt.edu>
To: gmx-users at gromacs.org
Sent: Wednesday, June 14, 2017 4:50:58 AM
Subject: Re: [gmx-users] Doubt about Free Energy control Minimization

On 6/13/17 4:31 PM, Varvdekar Bhagyesh Rajendra wrote:
> Dear Justin,
> 
> I aspire to derive energy-minimum structures when the interaction potential energy between the protein and the ligand are multiplied by 0.9, 0.8, 0.7,..., 0.2, 0.1.
> 
> I presume the following Free Energy minimization code mentioned in gromacs tutorial may do the trick. I would appreciate if you could please verify if it produces my intended result.
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/free_energy/Files/em_steep.mdp
> 

Possibly, but the outcomes may be unphysical.

-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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