I see. I'm using the V-rescaling thermostat in all simulations that I ran. I don't think I will use NPT for production run.
I'm trying to get NVE production run in the end. If I use NVT production run, I will try to account for the effect of the thermostat (I'm not sure I can do that very well). On Thu, Nov 6, 2014 at 10:47 AM, Mark Abraham <[email protected]> wrote: > Hi, > > Note that using the Berendsen thermostat in Gromacs adds defects for no > gain, compared with the Bussi v-rescale thermostat. The latter *is* > Berendsen, plus a stochastic term that produces the right energy and > velocity distributions (unlike Berendsen). I'd give serious consideration > to rejecting a paper that used Gromacs and the Berendsen thermostat, > particularly if they did not discuss why the known defects of Berendsen > were acceptable for their work. > > Mark > > On Thu, Nov 6, 2014 at 4:18 PM, Johnny Lu <[email protected]> wrote: > > > That post in the amber mailing list was quite interesting. May be using a > > weak berendsen thermostat in NVT is fine for them. Thanks for sharing > that. > > > > On Thu, Nov 6, 2014 at 6:39 AM, Johnny Lu <[email protected]> > wrote: > > > > > I was not offended by the suggestion. With a sufficiently large number > of > > > water molecules, the protein would behave in the same way, under all > > three > > > ensembles. > > > Barostat and thermostat are artificial in some way. At least, even the > > > diffusion coefficient is different in a force field paper that used > both > > > NVE and NVT. Langevin thermostat destroys some momentum transfer. > > > > > > This is my first paper, and I don't know if the reviewer will be fine > if > > I > > > report that my simulation has an average pressure of 11 bar with error > > 0.5 > > > bar. > > > > > > > > > On Thu, Nov 6, 2014 at 5:34 AM, Téletchéa Stéphane < > > > [email protected]> wrote: > > > > > >> Le 06/11/2014 06:16, Antonio Baptista a écrit : > > >> > > >>> > > >>> In particular, the virial-based "instantaneous pressure" (call it P') > > >>> computed in simulations has its ensemble average equal to the > > thermodynamic > > >>> pressure P (check any good book on molecular simulation). But, as > > others > > >>> already pointed out, this P' is well-known to show extremelly large > > >>> fluctuations, meaning that its average computed from the simulation > has > > >>> usually a very large statistical spread. In other words, although the > > >>> ensemble average of P' is strictly equal to P, its simulation average > > is a > > >>> random variable that often shows large deviations from P (especially > > for > > >>> short simulations). To get an idea of what is an acceptable error for > > the > > >>> average of P', you may look at its distribution histogram in the NPT > > >>> simulation. > > >>> > > >> > > >> Dear Antonio, > > >> > > >> Sorry if my message sound "aggressive" when I talked about "totally > > >> irrevelevant", I will clarify my thoughts. > > >> > > >> From a theoretical point of view, you are right, each ensemble is > > >> accessible. > > >> > > >> From a biological point of view, though, the concept of fixing the > > volume > > >> is less reasonable: > > >> we live at constant pressure and temperature, and also at tighly > > >> controlled pH, and salt concentrations. > > >> > > >> The volume varies though, as you feel it when the weather is getting > hot > > >> or cold. > > >> > > >> My point was exactly what your are telling in a more formal way than > me: > > >> "this P' is well-known to show extremely large fluctuations" > > >> > > >> Well, digging a bit more on my "feeling", I also found opposite > > arguments > > >> on the AMBER mailing list, > > >> like here: http://archive.ambermd.org/201103/0431.html > > >> > > >> So I'll got back again on my research and adjust my "mind" on the > actual > > >> bleeding edge simulations > > >> taking into account all the recent code and force fields progresses. > > >> > > >> Best, > > >> > > >> Stéphane > > >> > > >> -- > > >> Team Protein Design In Silico > > >> UFIP, UMR 6286 CNRS, > > >> UFR Sciences et Techniques, > > >> 2, rue de la Houssinière, Bât. 25, > > >> 44322 Nantes cedex 03, France > > >> Tél : +33 251 125 636 > > >> Fax : +33 251 125 632 > > >> http://www.ufip.univ-nantes.fr/ - http://www.steletch.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 [email protected]. > > >> > > > > > > > > -- > > 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 [email protected]. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? 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