[gmx-users] Re: generating user-defined topologies for surfaces

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441

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