[gmx-users] Continuous polymer chain?

David van der Spoel spoel at xray.bmc.uu.se
Fri Feb 6 19:55:02 CET 2009

Joshua Ballanco wrote:
> Hello all,
> Apologies if this is obvious, but I've been reading through the manual 
> and various Google searches and come up empty-handed. My question is if 
> it is possible to construct an infinite polymer chain in Gromacs? That 
> is, I'd like to setup a cell with PBC, but have one end of my molecule 
> bound to its replica across the boundary. As far as I can tell, adding 
> extra bond records to the topology always turns my polymer into a loop 
> in one cell.
use the mdp option periodic_molecules = yes

> Thank you for any advice.
> Sincerely,
> Joshua Ballanco
> Graduate Student
> Department of Chemistry and Chemical Biology
> Stevens Institute of Technology
> Hoboken, NJ 07030
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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