[gmx-users] polymer simulation

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 26 14:39:01 CEST 2003

On Thu, 2003-06-26 at 14:11, konradpi at poczta.onet.pl wrote:
> Hello all,
> I use gromacs for my polymer simulations and have two questions about that:
> - does anyone know good parameters for poly-alkylo-thiophenes, especially for sulfur in thiophene ring and the connection between ring and alkyl.
> - providing I have got right parameters for one mer, what is the common way to generate a topology for polymer (20-mers eg). I tried to develop my own itp file for one mer and a generator, that duplicates it, but it is not easy. Would it be easier to create a new residue and use pdb2gmx? (In manual I was discouraged about that)
if you have a few monomer types then pdb2gmx is the easiest way.
you need to make
rtp entry
hdb entry
and to do something about the ends., for proteins that's handled in 
XXX-c.tdb and XXX-n.tdb files.

Alternatively you can write a script that generates a topology (only if
it is very simple) or evenuse the x2top program (but that requires
hacking in files too, look for a XXX.n2t file).

> thanks for any help
> Konrad Piwowarczyk
> Faculty of Physics and Nuclear Techniques
> AGH University of Science and Technology, Kraków Poland
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Groeten, David.
Dr. David van der Spoel, 	Dept. of Cell & Mol. Biology
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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