On Mon, Dec 16, 2013 at 3:19 AM, Mahboobeh Eslami < mahboobeh.esl...@yahoo.com> wrote:
> hi all my friends > i am studying protein-ligand complex by gromacs 4.6.3 > i see followingText in gromacs site: > > Berendsen is often the best algorithm for equilibration, because it is > the most robust to the volume changes that might be expected during > equilibration. However it does not generate the proper thermodynamic > ensemble, so once the volume has stabilized, another method should be > used to equilibrate into the right ensemble. > > can i use two NPT equilibration and can i use Berendsen > andParrinello-Rahman for them? > thanks for your help > Sounds reasonable. That's basically what the manual is telling you. I often find the Berendsen barostat to be unnecessary, as NVT with the Berendsen thermostat, followed by NPT with Nose-Hoover or V-rescale for the thermostat and Parrinello-Rahman for the barostat is stable enough. That may not necessarily be the case every time, though, so one should not be fooled into thinking there are absolute rules here. -Justin -- ========================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ========================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.