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). > 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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