I forgot to ask, in additio to below, where to find the .itp file for cg water. All that I have is water.gro water.mdp water.top from the martini web site.
---------- Forwarded message ---------- From: Francesco Pietra <francesco.pie...@accademialucchese.it> Date: Tue, Dec 1, 2009 at 6:15 PM Subject: Re: [gmx-users] Last step before CG em.mdp To: jalem...@vt.edu, Discussion list for GROMACS users <gmx-users@gromacs.org> On Mon, Nov 30, 2009 at 5:51 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Francesco Pietra wrote: >> cpp = /usr/bin/cpp >> define = -DFLEX_SPC > > You're using SPC water in a coarse grain model? This doesn't make sense to > me - an atomistic solvent with CG protein? In order to use this em.mdp, how to "define" cg water? Otherwise, is it necessary at all to define the water used once there is a top file? > > It's been many weeks now that you've posted some issues with your CG system, > and I'm sorry but I can't recall - have you run through my membrane protein > tutorial? It should be easily quite extended to a CG system. All of the > fundamentals are the same as far as positioning the system, etc. go: > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html My task is more complex than that, where you immerse the whole peptide into the membrane. Actually, this is not my only interest, and I shift there when I find some spare time. Also, I succeeded by using martini as implemented into namd-vmd, but I would like to compare with gromacs. thanks francesco -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
