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

[XAvier Periole]

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.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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