[gmx-users] Centre of mass removal in CGMD

[Anirban Ghosh]

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
-------------------------------------------------------------------------------------------------

Any suggestion is welcome. Thanks a lot in advance.


Regards,

Anirban
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100813/168c6157/attachment.html>