Justin, I was speaking only about the bonded (and presumably, harmonic) potentials. Decreasing the time-step, as I mentioned, never made the things worse.
Vitaly On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Dr. Vitaly V. Chaban wrote: >> >> Hello Juliette: >> >> If you observe such behavior, I would suggest just to decrease a >> time-step. You should have the same energies at all temperatures. >> >> The larger is a time-step, the larger is a deviation from the energy >> minimum (bonded potentials). The larger is the deviation, the higher >> energy/force arises in order to get back to the equilibrium. >> >> > > Shorter time steps may be necessary to maintain stability of the system and > to conserve energy, certainly, but I don't understand your point about the > energy being independent of temperature. Increasing temperature should, in > theory, lead to excited states for bonds so they should be of higher energy. > For NVE, temperature fluctuations and compensatory potential changes keep > the energy constant, but at different temperatures, NVT and NPT ensembles > will inherently have different energies (and techniques like REMD derive > their usefulness in part from this fact). > > A given system should have a constant total energy, but I would certainly > expect a system run at 300 K to have a different total energy from one at > 400 K. > > -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
