[gmx-users] Continuous polymer chain?

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 6 19:20:27 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.

Depending on your Gromacs version, the approach will be different.  Under 3.3.x 
you can use "pbc = full," and provided that your topology is correct, you will 
get an infinite molecule.  Under 4.x (if I understand the changes correctly), 
you should be able to set "periodic_molecule = yes" in conjunction with "pbc = xyz."


> 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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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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