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.
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