I've used double precision. Today I'll copied output because it's done on lab comp but from the output log I've found that minimization was not completed ( e.g when I've calculate Normal Modes with that minimized structure I've obtain message that my system was not minimized properly )
2011/10/26 Justin A. Lemkul <jalem...@vt.edu> > > > James Starlight wrote: > >> Justin, >> >> >> I've forced with the problem that I could not prorerly minimized my system >> in the NMA conditions. Even in STEEP minimizaation I could not obtain Epot >> value lower than +3.00 with that parametries ( I've used KALP peptide as a >> test input ) >> >> > The Epot value is less significant than Fmax (which is what is set in the > .mdp file, anyway). What Fmax do you achieve? Real copied and pasted > output would be useful. > > > ; Parameters describing what to do, when to stop and what to save >> integrator = steep emtol = 1 ; Stop minimization when >> the maximum force < 1.0 kJ/mol/nm >> emstep = 0.01 ; Energy step size >> nsteps = 5000000 ; Maximum number of (minimization) steps >> to perform >> >> >> >> ; Parameters describing how to find the neighbors of each atom and how to >> calculate the interactions >> nstlist = 1 ; Frequency to update the neighbor list and long >> range forces >> ns_type = grid ; Method to determine neighbor list (simple, >> grid) >> rlist = 1.2 ; Cut-off for making neighbor list (short range >> forces) >> coulombtype = Shift rcoulomb = 1.0 >> rcoulomb_switch = 0.0 >> vdwtype = Shift >> rvdw = 1.0 >> rvdw_switch = 0.0 >> Than I've tried to futher minimized this structure via l-bfgs algorithm >> by >> >> integrator = l-bfgs >> dt = 0.01 >> emtol = 0.001 ; >> emstep = 0.1 ; Energy step size >> nsteps = 50000000 ; Maximum number of (minimization) steps >> to perform >> >> but Epot was still big. >> >> What I've done wrong ? >> > > Are you using single- or double-precision? > > -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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