On Tue, Jan 10, 2012 at 6:55 PM, Steven Neumann <s.neuman...@gmail.com>wrote:
> > > On Tue, Jan 10, 2012 at 6:22 PM, Justin A. Lemkul <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? > > > >> 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 ? > >> >> 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. > > 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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