[gmx-users] Inaccurate pressure readings

Denny Frost dsfrost at cableone.net
Tue Feb 1 21:22:24 CET 2011 

Sorry to revisit this subject, but this output does not make sense.  In the
log file from my NPT simulation, the pressure readings fluctuate between
about 300 bar and -300 bar, which I gather is pretty normal.  However, at
the end of the log file, it reports the average pressure being almost 1000
bar.  g_energy also reports this value.  In my mdp file, nstenergy is equal
to nstlog, so the frequency of data is the same in the .edr file.  How is is
possible that the final average would be greater than any value obtained
during the simulation?

On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  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>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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>
>
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