[gmx-users] Re: periodic molecule

Justin Lemkul jalemkul at vt.edu
Wed Sep 18 16:01:39 CEST 2013

On 9/18/13 9:57 AM, Valentina wrote:
> Bonds are harmonic. I can test it by restraining them? For purpose of testing
> I can even make the topology bond to be 2.06, as in the input file.

Constraints would probably fail, given the relatively large change in geometry. 
  You can try, but I'd suspect it will crash.

> My system shouldn't be any different from a mice sheet, for instance. Both
> have Metal - O bonds that continue through the sheet. What do you mean by
> "the original geometry" - obv it shall be slightly changing through the MD.

Original geometry = what you are providing for coordinates.

> Shall I be on Gromacs Dev sub-forum to get more insights on how the
> periodic_molecule works? Or may be could I ask person who implemented that
> part? I would really like to get it working in Gromacs, rather than having
> to change the engine.

If you want to talk about code, the development list is the right place for the 
discussion, but I know that periodic_molecules should work, given previous 
(solved) issues on the list and the fact that I made a simple CNT work at one 
point.  Have a look through the code and if there are any obvious (or 
non-obvious!) issues, please report back via gmx-developers.



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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