[gmx-users] How can I generate a Input *.gro file of coarse grain model?

He, Yang yang.he at mavs.uta.edu
Sun Oct 19 19:54:01 CEST 2008

Hi ,

I was also engaged in dealing with the problem about the course grain model . I find that in this CG force field , the potential functions almost don't correspond to that in the gromacs.

Hence, I wonder whether you know to how to define these new potential functions.

Thank you in advance.

From: gmx-users-bounces at gromacs.org [gmx-users-bounces at gromacs.org] On Behalf Of xuji [xuji at home.ipe.ac.cn]
Sent: Sunday, October 19, 2008 1:47 AM
To: gmx-users at gromacs.org
Subject: [gmx-users] How can I generate a Input *.gro file of coarse grain      model?

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 ]

[ 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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