[gmx-users] comm-grps for a membrane-protein-ligand system
Justin A. Lemkul
jalemkul at vt.edu
Mon Apr 11 19:58:24 CEST 2011
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.
> 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 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
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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