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

[Tsjerk Wassenaar]

Hi Xuji,

You'll have to have a coordinate file to start with, just like with
your atomistic scale stuff. Whether this would be .pdb or .gro doesn't
matter. If you have don't have coordinates, parameters are pretty
useless. Maybe the Groningen guys are willingg to share you a .pdb
file to play with. (Maybe the Groningen guys could write a
comprehensive tutorial for the Martini stuff, to be linked on the
wiki...).

Cheers,

Tsjerk

On Sun, Oct 19, 2008 at 10:47 AM, xuji <xuji at home.ipe.ac.cn> 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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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623