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
