>> 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. > As has been mentioned a number of times 0.9 +- 190 and 2.3 +- 190 are not > statistically different. If you use that in a publication then any > conclusions based on that will be rejected.
Statistically, I understood the indistinguishable difference between the resulted average pressures. Here, I altered tau_p values to determine if tau_p helps stabilize a desired value of average pressure. > > To demonstrate to yourself how variable the pressure is, the tau_p=1 run, > run the pressure analysis again using g_analyze, but using only the first > half and the last half of the trajectory. You will find that the average > values for both parts of the trajectory are not the same. > Thank you for the suggestion of applying g_analyze to trajectory. >> 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 > > That is not due to the pressure coupling. The changed box-size is problematic because I see that molecules are split. During NPT process, the box of dimensions (7.12158 7.14945 9.00000) changed over time to the end at that of dimensions ( 6.43804 6.46323 8.28666). This is because of pressure coupling. See noted also http://www.gromacs.org/Documentation/Errors#The_cut-off_length_is_longer_than_half_the_shortest_box_vector_or_longer_than_the_smallest_box_diagonal_element._Increase_the_box_size_or_decrease_rlist > Motion of the protein within the > box is simply due to diffusion etc. Also remember, that you have in > effect > an infinite repeating box in all directions, so the "center" of the box is > arbitrary. If so, how to make a membrane protein relatively fixed (embedded) in bilayer wthout escaping away during simulation ? In fact, this membrane has been embedded in membrane by g_membed. Due to diffusion ?? the protein moved away from bilayer and escaped toward extracellular space. Is there a way to fix it or only allow this protein diffusing in xy plane instead of z direction ? > If you want the protein to remain in the center for > visualisation purposes, then you do post processing on the box using > trjconv. > Thanks, but this dose not change the fact that protein moved away bilayer during a long simulation. >> 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. > > If you want fixed box dimensions / volume then you perform NVT. But that > will not help with either issues above. > Right. The box of dimensions remains unchanged if pressure coupling is removed in production MD. However, can it be justified in a system of membrane protein ? because the purpose of pressure coupling is to stabilize the pressure and density. For example, for 10 ns simulation, the average pressure of this system is -5.55 bar, which is less convincing. Energy Average Err.Est. RMSD Tot-Drift ------------------------------------------------------------------------------- Pressure -5.55572 2.6 155.552 0.846162 (bar) Thanks. Dwey > The problem here is you are trying to make comparisons in the behaviour of > simulations where there will not be a statistically significant difference > in the property you are adjusting. Any differences you observe are more > than likely going to be due to chance, rather than pressure. > > Catch ya, > > Dr. Dallas Warren > Drug Delivery, Disposition and Dynamics > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3052 > [hidden email] > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > -- > gmx-users mailing list [hidden email] > 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 [hidden email]. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > ________________________________ > If you reply to this email, your message will be added to the discussion > below: > http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011139.html > To unsubscribe from average pressure of a system, click here. > NAML -- View this message in context: http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system-tp5011095p5011155.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