> A pressure without an error bar is a meaningless value. The fluctuations > of pressure in most systems are on the order of tens or hundreds of bar, > meaning your result is indistinguishable from the target value.
To help illustrate this, here is one example of the type of pressure fluctuation you can get. https://twitter.com/dr_dbw/status/968624615063937025 Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. On Fri, 9 Nov 2018 at 00:01, Justin Lemkul <jalem...@vt.edu> wrote: > > > > On 11/8/18 7:50 AM, Gonzalez Fernandez, Cristina wrote: > > Dear Gromacs users, > > > > In my simulations, I have specified ref_p= 1bar but after MD simulation I > > obtain pressures equal to 0.19 bar (even > > A pressure without an error bar is a meaningless value. The fluctuations > of pressure in most systems are on the order of tens or hundreds of bar, > meaning your result is indistinguishable from the target value. > > > with long simulation times) when using pcoupl=Parrinello-Rahman. I know > > that Parrinello-Rahman is recommend for production runs and Berendsen for > > NPT equilibration. However, I have read in an article that > > Parrinello-Rahman is not stable for low pressures, so in such situations > > its better to use Berendsen. I have tried to use Berendsen for > > I would be interested to know how this "not stable for low pressures" > was determined, because it seems completely unlikely to be true. Most MD > simulations nowadays use Parrinello-Rahman for pressure coupling at 1 > bar/1 atm without any issue if the system is properly equilibrated (and > if not, the problem is with preparation, not the barostat itself). > > > MD simulation but I obtain this Warning and I cannot remove it with the > > -maxwarn option. > > > > "Using Berendsen pressure coupling invalidates the true ensemble for the > > thermostat" > > > > > > How can I use Berendsen for MD simulation? > > Simply, you can't, and you shouldn't. The Berendsen method produces an > invalid statistical mechanical ensemble. It relaxes systems quickly and > is therefore still useful for equilibration, but should never be > employed during data collection. Full stop. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.thelemkullab.com > > ================================================== > > -- > 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. -- 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.