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].
