Denny Frost dsfrost at cableone.net
Fri Jan 21 00:12:37 CET 2011

```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 <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
>
> +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] *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>
> 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
>
> +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] *On Behalf Of *Denny Frost
> *Sent:* Friday, 21 January 2011 9:07 AM
> *To:* 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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