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

[Justin A. Lemkul]

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
>>
>> ========================================
>> -- 
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the 
>> www interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 

-- 
========================================

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

========================================