[gmx-users] Centre of mass removal in CGMD

[Anirban Ghosh]

Thanks a lot XAvier. And if one wants to study the self assembly of a GPCR
using CGMD (like you did for rhodopsin), should he/she use the same
parameters for COM motion removal?


Regards,

Anirban

On Fri, Aug 13, 2010 at 3:18 PM, XAvier Periole <x.periole at rug.nl> wrote:

>
> 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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