[gmx-users] Re: Building a box pure solvent with genbox for CG simulations

[ABEL Stephane 175950]

Many Thanks Tsjerk, 

It works

A bientot

Stephane
------------------------------

Message: 3
Date: Mon, 25 Feb 2013 13:51:53 +0100
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
Subject: Re: [gmx-users] Building a box pure solvent with genbox for
        CG      simulations
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Message-ID:
        <CABzE1Sj95GDf-7QjhBekmjsk79RqH2ffP2+s5hBydVXZx4a4qw at mail.gmail.com>
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Hi Stephane,

martinize.py was written to convert proteins. But you can just take
C2+C5+C8 from atomistic decane and energy minimize against the martini
topology and you'll be fine.

Cheers,

Tsjerk

On Mon, Feb 25, 2013 at 1:39 PM, ABEL Stephane 175950
<Stephane.ABEL at cea.fr> wrote:
> Hello All,
>
> It is a newbie question here, but I can not find a clear response. I would like to create a simple box of pure DECANE for MD with the Martini force field. I have tried do that with genbox (as for AA force field)
>
> genbox_mpi -cp 1_CG_DECANE.pdb -ci 1_CG_DECANE.pdb -o CG_DECANE_box.gro -box 4.8 4.8 4.8 -nmol 255 -vdwd 0.21
>
> where 1_CG_DECANE.pdb file contains three atoms (or beads) for decane. This atoms C1, C2 and C3 are placed according the geometry given in the martini_v2.0_solvents.itp file (i.e distance between beads of 4.7 A and angle of 180o). With this command, only the first atom of the DEC molecule is added in the box.
>
> So how to construct of pure solvent when i use the Martini force field
>
> In addition i have tried to use the martinize python script to transform a box of decane (AA) -> CG, but seemes to work only for proteins (correct ?).
>
> Thank you in advance for your help
>
> Stephane
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--
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Biocomputing Group
Department of Biological Sciences
2500 University Drive NW
Calgary, AB T2N 1N4
Canada