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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