[gmx-users] Coupling groups - Thermostat

[Justin A. Lemkul]

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.

-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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