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

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Feb 25 13:51:53 CET 2013

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.



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

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