[gmx-users] Inaccurate pressure readings

[Mark Abraham]

On 21/01/2011 10:12 AM, Denny Frost wrote:
> 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.

In addition to all the points Justin mentioned, I'd observe that you're 
generating velocities at the start of the run, so the system will not be 
equilibrated for some time after that. See the advice here 
www.gromacs.org/Documentation/How-tos/Steps_to_Perform_a_Simulation. 
Anyway, you don't want to collect data for averages until after 
equilibration.

Secondly, tau-t of 0.1 is useful for equilibration, but a bit too 
stringent for actual simulations. Using v-rescale T-coupling is probably 
a good idea too.

Until you address all these issues about the numerical quality of your 
model of reality, hoping for observables to correlate with reality is 
not justified.

Mark

>
> On Thu, Jan 20, 2011 at 3:51 PM, Dallas Warren 
> <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> 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
>     dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
>     +61 3 9903 9304
>     ---------------------------------
>     When the only tool you own is a hammer, every problem begins to
>     resemble a nail.
>
>     *From:*gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org>
>     [mailto:gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org>] *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
>     <Dallas.Warren at monash.edu <mailto:Dallas.Warren at monash.edu>> 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
>     dallas.warren at monash.edu <mailto:dallas.warren at monash.edu>
>
>     +61 3 9903 9304
>     ---------------------------------
>     When the only tool you own is a hammer, every problem begins to
>     resemble a nail.
>
>     *From:*gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org>
>     [mailto:gmx-users-bounces at gromacs.org
>     <mailto:gmx-users-bounces at gromacs.org>] *On Behalf Of *Denny Frost
>     *Sent:* Friday, 21 January 2011 9:07 AM
>     *To:* gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
>     *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
>
>
>     --
>
>
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