[gmx-users] comm-grps for a membrane-protein-ligand system

Justin A. Lemkul jalemkul at vt.edu
Mon Apr 11 14:00:39 CEST 2011

Peter C. Lai wrote:
> Should I couple a ligand associated with a membrane protein to the same
> COM group as the Protein_POPC group? It makes sense to me that would be the 
> case since if we are investigating the interaction between protein+membrane 
> and ligand we want to have the same COM correction vector applied to both 
> relative to SOL_Ions but I just wanted to make sure...

If specifying multiple groups for COM motion removal, yes, the intuitive 
solution is to group the ligand with the protein (since they're physically 
bound, presumably).  The general complication is whether or not multiple COM 
groups are necessary - if the protein protrudes out into the solvent in any 
substantial way, you could have instability when the solvent and 
protein/membrane COMs get re-set.  I have seen this before in the case of a 
protein in water with separate COM groups (which is not appropriate, for the 
record).  Membrane systems are somewhat more complicated because they form 
interfaces that can slide, but if the protein somehow affects this behavior, 
well, I don't know that there's a trivial solution other than "comm_grps = 
System" to avoid possible instability.  If you're interested in 
diffusion-related properties, on the other hand, that may not be appropriate. 
Plenty to think about, but again, probably no "easy" solution.



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


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