[gmx-users] About the use of Gromacs as polymeric membranes simulator

David van der Spoel spoel at xray.bmc.uu.se
Mon Oct 13 19:59:44 CEST 2008

Inigo Garcia Yoldi wrote:
> Dear Gromacs User.
> I have recently started a project related with polymeric membranes 
> simulation for calculate some properties like the diffusion 
> coefficient//, permeability, solubility... The software that my group is 
> using right now is Accelrys "Materials Studio" but we have a serious 
> lack of licenses for massive calculation, then I have started to look 
> for alternatives and I have found Gromacs.
> The point is that I have found all the Gromacs tutorials focused to the 
> usage as Protein Simulator and I would like to know if someone is using 
> gromacs as Polymer Simulator; if so I will be very grateful if he can 
> help me about some points:
> 1) How to define the fragments of a polymer pdb file?
> 2) What is the more convenient force field for dealing with polymers?
> Any tutorial for the calculation of polymers in gromacs or any 
> recomendation about other software for this kind of simulation will be 
> welcome.

In fact one of the (old) benchmarks contains a polymer system. For 
building your own polymers I would recommend reading chapter 5 of the 
manual. If your monomer consist of "normal" organic components you could 
use either OPLS or Amber like force fields, it is anyway a good idea to 
read literature. I'm not familiar with Materials Studio but maybe you 
can write out topology files in a readable form.

As a side note GROMACS is used extensively with coarse-grained polymers 
as well.

> Thanks in advance.,
> I.
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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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