[gmx-users] Positive potential energy during Energy minimization step

[Justin Lemkul]

On 8/8/14, 7:25 AM, neha bharti wrote:
> I am trying to perform MD for protein ligand protein complex in popc lipid
> with charmm36 force field and also follow Justin A. Lemkul tutorial.
>
> After Adding Ion
>
> genion -s ions.tpr -o pro_POPC_sol_ions.gro -p topol.top -pname NA -np 1
> -nname CL
>
> I preform energy minimization step. In energy minimization step I am
> getting possitive potential enargy:
>
> Steepest Descents converged to machine precision in 18 steps,
> but did not reach the requested Fmax < 1000.
> Potential Energy  =  6.1499341e+17
> Maximum force     =            inf on atom 3300
> Norm of force     =  5.4206209e+18
>
>
> its mention in the tutorial verify that the values of Epot and Fmax are
> reasonable before continuing
>
> I am trying alot but not able to fix the issue.
>
> Its mention in tutorial but I am not able to find the exactly what to do.
>

You have infinite force, so you have unresolvable atomic clashes.

-Justin

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

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

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
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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