[gmx-users] Coupling groups - Thermostat

Steven Neumann s.neumann08 at gmail.com
Tue Jan 10 20:40:20 CET 2012 

On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul <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>**> wrote:
>>
>>
>>
>>    On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul <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.



>
>>         If not, it doesn't make sense to me to couple them together. In
>>        reality, no group should ever be coupled independently, but
>>        limitations in thermostats make it necessary.
>>
>>
>>    Would you suggest specifing 3 groups in this case: Protein, Tube,
>>    Water_and_ions ?
>>
>>
> Sounds about as good as any approach.  It's where I'd start.
>
>
>
>>        Regarding the ligand, where is it?  Floating around in solvent,
>>        bound to the protein, or in the tube?  The answer to that
>>        question motivates how you treat it.
>>
>>    With this simulation there is no ligand. My next simulation will be
>>    with 10-20 ligands placed randomly around the protein. I want to
>>    assess the influence of lmy ligands to the stability of the protein,
>>    that is why I need a comparison (in water only and in water with
>>    ligands).
>>    I am wondering how to specify coupling groups in this case.
>>
>>
> I would consider the ligands part of the solvent, because at such a high
> concentration, really what you're dealing with is almost a cosolvent
> situation.  Another example of species that may mix differently, aggregate,
> deposit on different surfaces, etc.  If there is existing literature on
> this topic (or even something peripherally related), try established
> protocols.
>
> When I will add my ligands they will surely stack to the protein (maybe
> tube as well...) . No clue what will happen between my protein and the tube
> above.
>

Thank you,

Steven


> -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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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