Hi xuji,
I do not believe the scripts provided on the site deal with water.
That is, unfortunately, you cannot take and equilibrated atomistic
system and convert directly to the CG representation.
What you will have to do is go to the "test/model" system page and
download the pure water system. You can then use this as an input to
genbox program.
Cheers
Mitch
Quoting "Justin A. Lemkul" <[EMAIL PROTECTED]>:
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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