Peter C. Lai wrote:
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
There is no "center" to a periodic system. Molecules diffuse, there's no way
around it. If you try to apply some biasing force to fit some visualization
convenience, you're potentially damaging the simulation's integrity.
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).
Position restraints do not fix anything in place, they merely provide an energy
barrier that penalizes change. If your goal is simply to obtain a reasonably
equilibrated system, then there is no need for a force constant above about
1000, otherwise you may be overtly influencing the ability of your system to
respond to change.
-Justin
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
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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========================================
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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