[gmx-users] Inaccurate pressure readings
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 1 21:49:20 CET 2011
Denny Frost wrote:
> 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?
>
As I recall from the previous discussion, there were lots of things wrong with
your .mdp file and many things to troubleshoot. Can you please post:
1. The .mdp file you're using
2. The contents of the "AVERAGES" and "RMS FLUCTUATIONS" sections of your .log file
3. The g_energy output (not the header stuff, just the actual meaningful result)
-Justin
> On Thu, Jan 20, 2011 at 4:33 PM, Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto: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
> <http://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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>>
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>
>
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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