[gmx-users] Coupling groups - Thermostat
Mark Abraham
Mark.Abraham at anu.edu.au
Tue Jan 10 23:59:33 CET 2012
On 11/01/2012 6:52 AM, Justin A. Lemkul wrote:
>
>
> Steven Neumann wrote:
>>
>>
>> On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul <jalemkul at vt.edu
>> <mailto:jalemkul at vt.edu>> wrote:
>>
>>
>>
>> Steven Neumann wrote:
>>
>>
>>
>> On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann
>> <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>
>> <mailto:s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>>__>
>> wrote:
>>
>>
>>
>> On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul
>> <jalemkul at vt.edu <mailto:jalemkul at vt.edu>
>> <mailto:jalemkul at vt.edu <mailto:jalemkul at vt.edu>>> wrote:
>>
>>
>>
>> Steven Neumann wrote:
>>
>> Dear Gmx Users,
>> My system includes: ions, water, two tubes made of
>> carbon
>> atoms, protein.
>> I would like to run NVT (and then NPT) with position
>> restarined dynamics of my protein and tubes.
>> I am wondering whether this approach is good (two
>> coupling
>> groups: Protein_Tubes and Water_and_ions??
>> My thermostat in mdp file:
>> Temperature coupling is on
>>
>> tcoupl = V-rescale ;
>>
>> tc_grps = Protein_Tubes Water_and_ions ; two coupling
>> groups
>>
>> tau_t = 0.1 0.1 ; time constant
>>
>> ref_t = 298 298 ; reference temperature
>>
>> Please, let me know whether this apporach is ok. How
>> can I
>> set tc_grps when I want to add ligand?
>>
>>
>> I don't know a definitive answer here, so I'll throw
>> out some
>> ideas and hopefully stimulate some discussion. I create
>> tc_grps
>> based on species whose dynamics are intimately
>> linked. For
>> solvent, that includes water and ions. Are your
>> protein and
>> tube physically associated?
>>
>> They are not physically associated but I put my protein as
>> close as
>> possible to the tube and I want to run position restrained
>> dynamics
>> of my tube and first 4 residues of my protein (stimulating
>> attached
>> protein to my tube).
>>
>>
>> Will you suggest attaching my protein directly to my tube in
>> this case?
>>
>>
>>
>> I'm assuming by "attaching" you mean coupling in the same tc_grp? I
>> wouldn't. This is a complex case (and again, I don't know a true
>> answer here) - your system has the potential to be highly dynamic.
>> Say the protein and tube bind, in which case they would (in theory)
>> be coupled together. Say they never bind, and then if you couple
>> them together they shouldn't be. You don't know a priori which way
>> it will go.
>>
>>
>> No. I mean physically attached. That is why my first 4 resiudes are
>> closed to the tube and position restrained. The best would be to
>> attach it physically by sharing one atom. No clue how. My tube is a
>> representation of the rest of the protein assembly (I am interested
>> in the influence of charged "residues" represented by ions and non
>> charged by carbon atoms within my tube - position restrained dynamics
>> the tube) on my protein. What is more there is another tube above my
>> protein (not attached) and I am interested also on the influence of
>> those "residues" of the tube on my protein conformation. In future I
>> want to do Umrella Sampling pulling my tube above to see free energy
>> difference.
>>
>>
>
> It would have been better to state all of this up front ;)
>
> If you are trying to create a single entity representing the protein
> and the tube, then yes, they should be a single tc_grp, and the best
> approach is to create a merged [moleculetype] definition with an
> actual bond between the shared atoms. Doing so is not trivial, and I
> have no real quick way to suggest doing that, other than recreating a
> topology from pdb2gmx and perhaps making use of specbond.dat. I'm
> still not 100% clear on where everything is located.
>
> The other tube (not attached) and solvent/ions/ligands should likely
> be treated as separate groups for the purposes of temperature
> coupling. But again, as stated, this is a very complicated system and
> the best methodology for simulating it is likely not defined terribly
> well.
One alternative is to pay attention to the advice at the end of section
3.4.8 of the manual and ref cited there - that separate T-coupling
groups can be worse than the problems they purport to fix.
Mark
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