[gmx-users] infinite force at the membrane lipid

[Justin Lemkul]

On 8/15/15 12:41 PM, Vy Phan wrote:
> Dear All gromacs Users,
>
> I want to run the membrane protein simulation. I run the energy
> minimization for membrane and protein separately.
> After that I combine protein  and lipid together and remove the overlapping
> molecules.
> when I run energy minimization I got the error "inf at atom on lipid". I
> remove the lipid which includes this atom.  I got the error several time
> and I repeat remove lipid. I see the "inf at atom on lipid" always happens
> on lipids which locate at the wall (at the boundary of unit cell).
>
> I successfully run one time when I remove  lipids have error, another was
> failed.
>
> I wonder why the error "inf at atom on lipid" always happens on lipids
> which locate at the wall. Maybe I did something wrong about periodic
> boundary condition.
>
> Thank you for any thoughts.
>

Without a list of your exact commands and what you've done to this point, it's 
impossible to diagnose.  There's something fundamentally wrong with the 
coordinates, topology, or both.  If the infinite force is just moving around, 
what you're observing is a symptom, not a cause, and removing lipids to try to 
make it go away is not an appropriate solution.

-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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