Re: [gmx-users] Inaccurate pressure readings

Justin A. Lemkul Tue, 01 Feb 2011 12:50:07 -0800


Denny Frost wrote:

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

As I recall from the previous discussion, there were lots of things wrong withyour .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.abra...@anu.edu.au<mailto:mark.abra...@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.war...@monash.edu <mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@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-boun...@gromacs.org
        <mailto:gmx-users-boun...@gromacs.org>
        [mailto:gmx-users-boun...@gromacs.org
        <mailto:gmx-users-boun...@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.war...@monash.edu <mailto:dallas.war...@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.war...@monash.edu <mailto:dallas.war...@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-boun...@gromacs.org
        <mailto:gmx-users-boun...@gromacs.org>
        [mailto:gmx-users-boun...@gromacs.org
        <mailto:gmx-users-boun...@gromacs.org>] *On Behalf Of *Denny Frost
        *Sent:* Friday, 21 January 2011 9:07 AM
        *To:* gmx-users@gromacs.org <mailto:gmx-users@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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--
========================================

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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Re: [gmx-users] Inaccurate pressure readings

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