Hi! So the part of my pr.mdp files that handles pressure and temperature looks like as below and if I were to create an index file by name "N-extension" an type it next in the tc-grps as N-extension along with the existing Protein Non-Protein groups is this how I get to handle the simulated annealing for the appended NMR group? Thanks Jayant James
; Berendsen temperature coupling is on in two groups Tcoupl = berendsen tc-grps = Protein Non-Protein tau_t = 0.1 0.1 ref_t = 300 300 ; Energy monitoring energygrps = Protein Non-Protein ; Pressure coupling is not on Pcoupl = parrinello-rahman tau_p = 0.5 compressibility = 4.5e-5 ref_p = 1.0 On Sat, Mar 7, 2009 at 4:33 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > jayant james wrote: > >> Hi! >> I have appended the NMR structure to a part of the protein that was not >> resolved to the protein and now I want to perform simulated annealing of the >> 40 amino acids (NMR structure had 33 amino acids and to link I needed >> another 7 aa) that have been thrown into the crystal structure. I am new to >> this simulated annealing procedure. So please help me out as how to write >> out a typical pr.mdp file. I am thinking of increasing the temp of the >> appended piece protein piece to about 10000K (while the rest of the protein, >> solvent, Na+ and Cl- are at 300K) and slowly bring the temperature down to >> 300K, say, in about 100 ps and then continue to perform MD simulations. >> > > Running a protein segment at 10000 K with solvent at 300 K will probably > lead to some wild behavior of that protein segment, clashes with the > solvent, and possibly an explosion of your system. Just thinking ahead... > > 1) So would it be the wise time to apply distance constraints from the >> protein at 300K to the appended peptide while performing simulated >> annealing? >> > > If you have actual NMR data, perhaps. But attempting to simulate at 10000 > K while simultaneously applying distance restraints might be a difficult > task (consider a lower temperature). > > 2) If so what would be a good temperature to set it to kick in? I am really >> confused as to how I am going to specify these 40 residues to be the group >> that needs to be heated up. >> > > Warm it up from some low temperature. There is an example at: > > http://www.gromacs.org/documentation/reference_4.0/online/mdp_opt.html#sa > > If you want a separate temperature coupling group, make a special index > group for it. No idea if that will actually work, but that's how you treat > components of your system differently, in general. > > 3) Usually I have tc-grps specified in pr.mdp as Protein and Non-Protein. >> So how would I go about setting up the temperature groups during the >> simulated annealing protocol? >> > > With the special index group. See #2. > > -Justin > > Thanks >> JJ >> >> >> On Thu, Feb 26, 2009 at 4:47 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> jayant james wrote: >> >> Hi! >> I have a question with regard to a system that I am attempting >> to model. >> The N-terminal of chain of the protein was not resolved >> crystallographically but was later solved by NMR. >> Now my plan is to append the NMR structure on to chain A of the >> protein and perform simulated annealing only for the appended >> NMR fragment. To help it find it biologically relevent >> orientation in the system I could also apply distance restraints >> that I have. >> Is this possible in Gromacs? >> >> >> All except that actual construction part (modeling the two segments >> together), yes. >> >> -Justin >> >> thanks >> JJ >> >> >> >> ------------------------------------------------------------------------ >> >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Graduate Research Assistant >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu/> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> _______________________________________________ >> gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> http://www.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> >> >> -- >> Jayasundar Jayant James >> >> www.chick.com/reading/tracts/0096/0096_01.asp < >> http://www.chick.com/reading/tracts/0096/0096_01.asp>) >> >> > -- > ======================================== > > Justin A. Lemkul > Graduate Research Assistant > ICTAS Doctoral Scholar > > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/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/mailing_lists/users.php > -- Jayasundar Jayant James www.chick.com/reading/tracts/0096/0096_01.asp)
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