[gmx-users] Coupling groups - Thermostat

Justin A. Lemkul jalemkul at vt.edu
Tue Jan 10 20:52:49 CET 2012

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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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