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
MILES-IGERT Trainee
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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