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 <[EMAIL PROTECTED]> 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! > > > > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
