There are scripts provided on the MARTINI site to generate the necessary
structure files, and the topology, IIRC.
-Justin
xuji wrote:
Dear all gromacs users:
I am trying to use the MARTINI CG force field from Marrink et al. in my simulation.
But I don't konw how to generate the input *.gro files.
When I use all-atom model, in gromacs I can use "genbox" "editconf" et al to
generate
the input *.gro files. For example, I can use "genbox -cs -box 10 10 10 -o
waterbox.gro"
to generate pure water box. But if I only have the files downloaded from
"http://md.chem.rug.nl/~marrink/MARTINI/Parameters.html"; , and I use a *.top file
which contains:
#include "martini_v2.0.itp"
#include "martini_v2.0_lipids.itp"
[ system ]
DPPC BILAYER
[ molecules ]
DPPC 128
W 2000
Can I generate a *.gro file according to this topology file using Gromacs'
tools?
If can, how do it?
Appreciate any help in advance!
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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