On 7/31/13 8:57 AM, Valentina wrote:
Sorry, still confused here:
I have a cell, that is same as residue, contains an inorganic crystal. But
since I am creating a surface I have bonds going across periodic boundary,
like Al and O shown on the pic? Can I still do it? How do I input it into
molecule.rtp?
Construct the bond like you would any other bond. Then set "periodic_molecules
= yes" in the .mdp file.
-Justin
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Justin A. Lemkul, Ph.D.
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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