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

[Francesco Pietra]

Is anything recent to account for (and eliminate) clashes - if any -
resulting from solvating a system of protein partly immersed into a
canonical DPPC bilayer? That is, the solvation water  faces three
different environments: the extracellular portion of the protein, the
two water layers of DPPC, and the DPPC molecules themselves.

I was comfortable to this regard (in all-atoms) with Chimera followed
by Amber minimization. I have to re-educate myself with
gromacs-martini. With cg Chimera has so many limitations.

I assume (for cg) that the box should first be defined with editconf
and then solvation (-cs water.gro) carried out with genbox.

thanks
francesco



On Tue, Dec 1, 2009 at 6:37 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> 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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