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

XAvier Periole x.periole at rug.nl
Tue Dec 1 18:33:37 CET 2009

you do not need itp file. in the top you'd find the parameters for
the water.

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.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?
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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