[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
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
> Thanks in advance.,
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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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