On Dec 1, 2009, at 6:33 PM, XAvier Periole wrote:
you do not need itp file. in the top you'd find the parameters for
the water.
I mean in the top file you'll find the reference to the martini??.itp
file
where the water is defined.
On Dec 1, 2009, at 6:26 PM, Francesco Pietra wrote:
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?
no need to define.
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.
good idea.
thanks
francesco
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