[gmx-users] Re: periodic molecule

Justin Lemkul jalemkul at vt.edu
Wed Sep 18 15:44:14 CEST 2013

On 9/18/13 9:09 AM, Valentina wrote:
> Thank you,
> Yes.
> The bond between Al and O is 1.96 A
> So it should be within 10% from 2.06 A, so the lowest size is 1.854 A? It
> should be able to pick up 1.96 A then. Am I right?

In theory, that bond should work.  It looks like a pretty complex system though, 
so any number of things could be breaking.  Are your bonds constrained, or 
simple harmonic interactions?  If the latter, there is no guarantee that you can 
preserve the original geometry.  Check the inputs carefully (since this is a 
very non-standard application as far as "normal" Gromacs usage goes) and build 
the smallest test case you possibly can for each interaction.



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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