[gmx-users] problem of running multiple cores (Tom)
jalemkul at vt.edu
Sun Mar 16 00:33:43 CET 2014
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On 3/15/14, 7:27 PM, Tom wrote:
> Thanks for your quick response!
> Yes, I used "periodic_molecules = yes"
> It is correct to use this, right?
Per your description of bonds across PBC, yes. The periodic_molecules keyword
is intended for this exact situation (in fact, that's its only purpose).
> I just can not figuire out why single core can work but can not work
The DD algorithm can't resolve the bonded geometry, while in serial perhaps
something is coincidentally working.
> Is it because i did not assign the charge groups on my surface atoms?
No. If you didn't use periodic_molecules, that's why it's failing. It's not
entirely clear what you mean by "did not assign charge groups." Does that mean
all the atoms are in a single group, or each atom is in its own group? If the
former, you will have problems with neighbor searching unless you are using the
Verlet cutoff scheme. If the latter, there is no problem as long as you are
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
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