Justin Lemkul wrote > On 9/11/13 12:12 AM, Dwey Kauffman wrote: >>> True, but thermostats allow temperatures to oscillate on the order of a >>> few >> K, >>> and that doesn't happen on the macroscopic level either. Hence the >>> small >>> disconnect between a system that has thousands of atoms and one that has >>> millions or trillions. Pressure fluctuations decrease on the order of >> sqrt(N), >>> so the system size itself is a determining factor for the pressure >> fluctuations. >>> As previous discussions have rightly concluded, pressure is a somewhat >>> ill-defined quantity in molecular systems like these. >> >> Dose it also imply that it is not a good idea to study the relationship >> between dimer (multimer) dissociation and macroscopic pressure in this >> case >> ? (due to the ill defined pressure). >> > > I would simply think it would be very hard to draw any meaningful > conclusions if > they depend on a microscopic quantity that varies so strongly. > >> It is hard to be justified if I assign a set of various ref_p= 0.7, 0.8, >> 0.9, 1.0, 1.1, 1.2 ...., perform independent simulations, and then obtain >> outcomes of targeted quantities for comparison. >> > > As with the original issue, I would find it hard to believe that any of > the > differences observed in such a setup would be meaningful. Is 0.7 ± 100 > actually > different from 1.2 ± 100? > >>> >>> You could try altering tau_p, but I doubt there is any value in doing >>> so. >> >> I would give it a try. >> > > This will really only change the relaxation time. Smaller values of tau_p > may > improve the average slightly, but may also (more likely) lead to > instability, > especially with Parrinello-Rahman.
I carried out independent NPT processes with different tau_p values = 1.5, 1.0 and 0.5 ## tau_p 1.5 Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 2.62859 2.6 185.68 2.67572 (bar) ## tau_p 1.0 Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 0.886769 1.7 187.737 0.739 (bar) ## tau_p 0.5 Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure 2.39911 2.2 185.708 6.8189 (bar) ############################## It is clear that when tau_p =1.0, average pressure of the system (=0.89 bar) is close to ref_p =1.0 bar However, it is unclear to me as to how to assign a good value to tau_p in order to reach at a close value of ref_p. As shown above, both of the average pressures as tau_p =1.5 and 0.5 are much higher than that as tau_p =1.0. A smaller tau_p may or may not help. Another issue caused by system pressure is about pbc box size. Since I use pressure coupling, the box size is not fixed such that protein moved away the center of membrane for a long simulation like 30 ns. Box size changes significantly during production MD. Is there a way to fix the box size at the very beginning ? although turning off pressure coupling will make box size fixed. Best regards, Dwey -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011137.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
