[gmx-users] Problem in energy minimization

[Tsjerk Wassenaar]

Hi Jin,

Can you give the protocol you used in commands? And what are the box
dimensions and how many solvent molecules were added?

Cheers,

Tsjerk
On Jun 5, 2015 08:30, "Jin J.C" <jcjin.hcmut.001 at gmail.com> wrote:

> Dear Justin,
> I have tried to change the box size, make it smaller a little, solvate
> again and then, the error is resolved. Actually, I don't understand the
> reason. especially, I have no idea about the "impossible geometry" as you
> mentioned. Can you give me a little explanation?
> Thank you so much.
> Jin.
>
> 2015-06-04 20:38 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:
>
> >
> >
> > 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
> >
> > --
> > ==================================================
> >
> > 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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