On Tue, Jan 10, 2012 at 7:07 PM, Justin A. Lemkul <jalem...@vt.edu> wrote:
> > > Steven Neumann wrote: > >> >> >> On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann >> <s.neuman...@gmail.com<mailto: >> s.neuman...@gmail.com>**> wrote: >> >> >> >> On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto:jalem...@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> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<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-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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