[gmx-users] Centre of mass removal in CGMD

[XAvier Periole]

On Aug 13, 2010, at 10:00 AM, Anirban Ghosh wrote:

> Hi ALL,
>
> I am trying to simulate a protein inserted in a lipid bilayer with  
> water and ions, the entire system built using CG (coarse grain). I  
> am using the Martini force field to the CGMD simulation. My question  
> is that should I use the "centre of mass removal" component in  
> my .mdp file (which we do for an all-atom protein + lipid  
> simulation)? Should I use the below given parameters in my mdp file  
> for this CGMD simulation:
>
> -------------------------------------------------------------------------------------------------
> ; COM motion removal
> ; These options remove motion of the protein/bilayer relative to the  
> solvent/ions
> nstcomm		= 1
> comm-mode	= Linear
> comm-grps	= Protein_DSPC W
> -------------------------------------------------------------------------------------------------
This is the way to go :))
>
> Any suggestion is welcome. Thanks a lot in advance.
>
>
> Regards,
>
> Anirban
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