[gmx-users] Problem in energy minimization

[Justin Lemkul]

On 6/3/15 10:23 PM, Jin J.C wrote:
> Dear all,
> I am trying to set a coarse-grained MD for the membrane protein.
> After solvating, I met an error when running a short energy minimization (
> 10 steps) before adding ions.
>
> Steepest Descents:
> Tolerance (Fmax)   =  1.00000e+01
> Number of steps    =           10
> Step=   10, Dmax= 2.0e-05 nm, Epot=  2.76192e+20 Fmax=         inf, atom=
> 8872
> Reached the maximum number of steps before reaching Fmax < 10 writing
> lowest energy coordinates.
> Steepest Descents did not converge to Fmax < 10 in 11 steps.
> Potential Energy  =  2.7619190e+20
> Maximum force    =           inf on atom 8872
> Norm of force       =            inf
>
> The reason is because of Maximum force is equal to infinity. Therefore I
> can not proceed further. Atom 8872 is water atom. Even when I delete this
> atom, the error occurs again with another water molecules, and goes on.
>
> Can someone help me figure out? and explain to me what happen?  Is this
> because of overlapping problem?
>

Likely.  You have some impossible geometry somewhere, or otherwise something is 
very wrong with the topology.

-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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