Hey ;) For those, you really have to consider what the purpoase of the simulations is. For energy minimization it's getting rid of clashes that might cause the system to blow up. For NVT equilibration the aim is equilibrating the temperature, which is usually fast enough. For NpT it's equilibrating the pressure, which may take a bit more time, mainly because it fluctuates so wildly. Especially when aiming to do later simulations with parrinello-rahman pressure coupling, NpT equilibration requires a bit of care, and a Berendsen manostat. It's true that larger system take longer to relax, but the relaxation for these steps is fast enough anyway. The real trouble starts when equilibrating under production simulation conditions. There the size of the system is quite an issue, and relaxation times are usually (much) longer than you care for.
Cheers, Tsjerk On Wed, Apr 11, 2012 at 8:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Acoot Brett wrote: >> >> In the on-line tutorial of *Justin Lemkul >> *(http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/index.html) >> for both lysozyme, for the mini.mdp, nvt.mdp and npt.mdp, the nsteps = >> 50000. Do you think this valus is depend or independent of the molecular >> weight of the protein or not? >> > > > The length of the simulation depends on the amount of time needed for the > system to achieve whatever level of convergence is desired. System size can > play into this calculation, but I have never found it to be a significant > factor. > > -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 > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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
