Part answer is provided at http://www.gromacs.org/Documentation/Terminology/Pressure
Have you plotted how the pressure changes with time during your simulation? What you will notice is that the pressure is oscillating between something like +300 bar and -300 bar. With such large variations like that, is it not surprising that the average is not exactly 1? Catch ya, Dr. Dallas Warren Drug Discovery Biology Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3052 dallas.war...@monash.edu +61 3 9903 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. > -----Original Message----- > From: gmx-users-boun...@gromacs.org [mailto:gmx-users- > boun...@gromacs.org] On Behalf Of Dwey > Sent: Wednesday, 11 September 2013 11:12 AM > To: gmx-users@gromacs.org > Subject: [gmx-users] average pressure of a system > > Hi All. > > I work on a simulation of a membrane protein in a model membrane > (DPPC) with a total of 26,859 atoms. In a step of NPT equilibration, > my mdp file is used for a 100 ps NPT and it has a reference pressure > of 1 bar. > > At the end of simulation, I obtained a result of the average > pressure of the system ( ~ -0.90 bar) like > > Energy Average Err.Est. RMSD Tot-Drift > ----------------------------------------------------------------------- > -------- > Pressure -0.9049 2.6 186.304 13.8503 > (bar) > > > I am wondering if I should keep running this NPT process until the > average pressure of the system reaches ~ 1.0 bar. > > If so, how long ( how many steps) ? > > Or should I modify mdp file ? Can anyone provide some suggestions ? > > > Likewise, at the end of Production MD for 1 ns, I obtained average > pressure (~2.23 bar) of the system like > > Energy Average Err.Est. RMSD Tot-Drift > ----------------------------------------------------------------------- > -------- > Pressure 2.23349 2.1 164.97 10.9381 > (bar) > > Should I run a longer simulation until the average pressure reaches ~ > 1.0 bar, although average energy, average temperature (323 K), > average density (1022 kg/m^3) are already at the desired values ? > > How should I do to stabilize average pressure at a desired value (~1 > bar) ? > > > Thanks for any input. > Dwey > -- > 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 -- 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
