[gmx-users] comm-grps

Justin Lemkul jalemkul at vt.edu
Tue Feb 19 16:16:31 CET 2013

On 2/19/13 9:25 AM, fciocco wrote:
> Hi
> I want to study the interaction between a peptide and a lipid bilayer, with
> the peptide initialy outside de bilayer.  Is correct to choose only
> "bilayer" and "SOL_ions" as comm-groups ? because grompp complain about that
> with a warning: some atoms are not part of any center of mass motion removal
> group. This may lead to artifacts.

That setup leaves the protein unaccounted for, hence the warning from grompp. 
This is a tricky system to deal with, because the associations between molecules 
will change over time; it's not as easy as a pure membrane (where water and 
lipids might be in separate groups) or a protein in water (where the whole 
system is the only sensible group).  In my mind, the only appropriate setting 
here is "comm-grps = System."



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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