[gmx-users] Centre of mass removal in CGMD

Anirban Ghosh reach.anirban.ghosh at gmail.com
Fri Aug 13 10:00:12 CEST 2010


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
nstcomm = 1
comm-mode = Linear
comm-grps = Protein_DSPC W

Any suggestion is welcome. Thanks a lot in advance.


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