[gmx-users] Re: Software to generate polymer coordinates

Vitaly Chaban vvchaban at gmail.com
Wed Aug 18 09:20:11 CEST 2010

Dear Dallas:

Very useful question, I'm also interested. At the very basic level,
GENCONF (gromacs utility) can be used to replicate monomer. One should
pay much attention for the size of the elementary box then. The next
quest is to force X2TOP to recognize bonds where they are. If you
succeed with topology, then try energy minimization with MDRUN and the
polymer hopefully is ready.

If you find a more robust way, please let us know.


Dr. Vitaly Chaban

> I have been searching for awhile now trying to find a script / software
> package that will generate the coordinates of a polymer.  There are some
> that will repeat a simple unit and there is an online one that will
> allow you to generate some, but you can only use their predefined
> monomers (http://wwmm-svc.ch.cam.ac.uk/polydemo/).
> What I am after is something that you can specify your own monomer
> units, how they link together, able to handle more than one monomer,
> manner in which monomers are bonded (alternating, periodic, statistical,
> block) and may be even grafts.
> Has anyone found or know of one that can do anything like this?
> Catch ya,
> Dr. Dallas Warren
> Drug Delivery, Disposition and Dynamics
> Monash Institute of Pharmaceutical Sciences, Monash University
> 381 Royal Parade, Parkville VIC 3010
> dallas.warren at pharm.monash.edu.au
> +61 3 9903 9167

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