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

Peter C. Lai pcl at uab.edu
Mon Apr 11 17:57:58 CEST 2011

Ok thanks

My primary concern is to cancel membrane-protein drift - the protein
getting pushed to one side of the membrane box (also it's important for
me to have the protein stay centered in the box too). I have not seen 
stability issues otherwise with COM turned on in the case of the unbound 
protein and the membrane as separate COM groups. The only instability 
I have encountered thus far is LINCS crashing due to too much forces if
I set the restraint forces too high (like 100000 kJ/mol), but I've resigned
myself to the fact that the residual RMS drift appears acceptable at the end
of membrane/solvent equilibration runs if I drop it down to 10000 kJ/mol
during NPT equilibration).

On 2011-04-11 07:00:39AM -0500, Justin A. Lemkul wrote:
> 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
> -- 
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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Peter C. Lai                 | University of Alabama-Birmingham
Programmer/Analyst           | BEC 257
Genetics, Div. of Research   | 1150 10th Avenue South
pcl at uab.edu                  | Birmingham AL 35294-4461
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