Sorry, I'm referring to a lot of runs here - some fluctuate more than others and some have greater average values than others. The average value is never greater than the maximum fluctuation in each run, so that is not a problem. The average given by g_energy, however, is not close to 1.0 bar in any of my runs. Some runs give an average pressure of 10 bar, some give an average value of -1000 bar.
On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren <[email protected]>wrote: > Then something you have said isn’t right. In first email you said that the > pressure varies between -400 and +400 bar. Now you say that the average can > vary from -1000 to +1000 bar. If the instantaneous pressure is varying from > -1000 to +1000 bar, then that is not a real issue. However, if the average > can be from -1000 to +1000 bar, then that definitely is. > > > Which one is it? > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > [email protected] > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Denny Frost > *Sent:* Friday, 21 January 2011 9:23 AM > *To:* Discussion list for GROMACS users > *Subject:* Re: [gmx-users] Inaccurate pressure readings > > > > The average I calculate is not within -10 to 10, it is on the order of > -1000 to 1000 > > On Thu, Jan 20, 2011 at 3:11 PM, Dallas Warren <[email protected]> > wrote: > > You have a variable that is fluctuating over a range of 800+ units (three > orders of magnitude) and want the average to be 1.0? > > > > It is not a problem as such. If you can get a large enough data set of > pressure data, and it will have to be very large, then you might get it > close to one. > > > > But as long the average you calculate is within may be an order of > magnitude (-10 to 10) then there is nothing to get too worried about. > > > > Catch ya, > > Dr. Dallas Warren > > Medicinal Chemistry and Drug Action > > Monash Institute of Pharmaceutical Sciences, Monash University > 381 Royal Parade, Parkville VIC 3010 > [email protected] > > +61 3 9903 9304 > --------------------------------- > When the only tool you own is a hammer, every problem begins to resemble a > nail. > > > > *From:* [email protected] [mailto: > [email protected]] *On Behalf Of *Denny Frost > *Sent:* Friday, 21 January 2011 9:07 AM > *To:* [email protected] > *Subject:* [gmx-users] Inaccurate pressure readings > > > > I am running a variety of NPT simulations with polar, non-polar, and ionic > compounds. Although my results for density agree well with experimental > values, the pressures I get from g_energy are off by 1 to 3 orders of > magnitude. In the log file, the pressure fluctuates around a lot from -400 > to 400 bar, which seems to be normal according to other posts on this list, > but the average (which is what g_energy gives me) is not 1.0 bar, as I > specified. Does anyone know how to correct this problem? > > > > Pressure coupling parameters: > > Pcoupl = berendsen > > pcoupltype = isotropic > > tau_p = 1.0 > > ref_p = 1.0 > > compressibility = 4.5e-5 > > > -- > > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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