If the problem of using a 11 bar simulation is as big as the problem of drawing conclusion from a single simulation, I guess I have to get a pressure closer to 1 bar. Thanks.
On Thu, Nov 6, 2014 at 10:55 AM, Johnny Lu <[email protected]> wrote: > 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? 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