Also remember that here you are dealing with the measurement of a macroscopic property on a microscopic scale.
As Justin has alluded to, the only manner in which you can make the variation / fluctuations in the pressure smaller is by increase the total number of particles in the system. Catch ya, Dr. Dallas Warren Drug Delivery, Disposition and Dynamics 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 Kauffman > Sent: Wednesday, 11 September 2013 12:57 PM > To: gmx-users@gromacs.org > Subject: [gmx-users] RE: average pressure of a system > > Hi Dallas and Justin, > > Thanks for the reply. Yes, I did plot pressure changes over time by > g_energy and I have been aware of the note at > http://www.gromacs.org/Documentation/Terminology/Pressure > > I am concerned about the average pressure is because our experiment > shows > that our target membrane protein is a hexamer and our observation is > that > variation of system pressure seems causing hexamer or dimer > dissociation. > Also, it is quite sensitive to pressure fluctuation. Such a fluctuation > of > pressure certainly brings my attention in this specific case, because > life > does not exist at large variations of system pressure. > If not because of multimer dissociation likely caused by pressure > fluctuation, I agree with both of you. > > I also run longer simulations like 20 ns and 30 ns > > ### 20 ns > > Energy Average Err.Est. RMSD Tot-Drift > ----------------------------------------------------------------------- > -------- > Pressure 0.886396 0.84 162.655 1.38476 > (bar) > > ## 30 ns > > Energy Average Err.Est. RMSD Tot-Drift > ----------------------------------------------------------------------- > -------- > Pressure 1.69086 0.58 162.879 3.35668 > (bar) > > > Running longer simulations seems to me that the improvement of system > pressure is not helpful too much. > If I need to modify mdp file, what it would be ? > > > > Many thanks, > > Dwey > > > My mdp file for NPT is used in the simulation like > > define = -DPOSRES > > integrator = md > nsteps = 500000 > dt = 0.002 > > nstxout = 100 > nstvout = 100 > nstenergy = 100 > nstlog = 100 > > continuation = yes > constraint_algorithm = lincs > constraints = all-bonds > lincs_iter = 1 > lincs_order = 4 > > ns_type = grid > nstlist = 5 > rlist = 1.2 > rcoulomb = 1.2 > rvdw = 1.2 > > coulombtype = PME > pme_order = 4 > fourierspacing = 0.16 > > tcoupl = Nose-Hoover > tc-grps = Protein DPPC SOL_CL > tau_t = 0.5 0.5 0.5 > ref_t = 323 323 323 > > pcoupl = Parrinello-Rahman > pcoupltype = semiisotropic > tau_p = 5.0 > ref_p = 1.0 1.0 > compressibility = 4.5e-5 4.5e-5 > > pbc = xyz > > DispCorr = EnerPres > > gen_vel = no > > > nstcomm = 1 > comm-mode = Linear > comm-grps = Protein_DPPC SOL_CL > > refcoord_scaling = com > cutoff-scheme = Verlet > > > > > > > > > > > > > > > > > > -- > View this message in context: > http://gromacs.5086.x6.nabble.com/average-pressure-of-a-system- > tp5011095p5011098.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 -- 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
