Fwd: [gmx-users] Last step before CG em.mdp

Francesco Pietra francesco.pietra at accademialucchese.it
Tue Dec 1 18:26:05 CET 2009

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.pietra at accademialucchese.it>
Date: Tue, Dec 1, 2009 at 6:15 PM
Subject: Re: [gmx-users] Last step before CG em.mdp
To: jalemkul at vt.edu, Discussion list for GROMACS users <gmx-users at gromacs.org>

On Mon, Nov 30, 2009 at 5:51 PM, Justin A. Lemkul <jalemkul at 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.


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