[gmx-users] Inaccurate pressure readings
Justin A. Lemkul
jalemkul at vt.edu
Wed Feb 2 00:01:04 CET 2011
Denny Frost wrote:
> Sorry about that, I tried to delete that post because it was too long.
> The mdp file used to generate that data in the xvg file was the same
> except for the nsteps parameter. Also, I copied that file from excel
> where I was analyzing it and didn't realize until afterward that it had
> cut off the first digit starting with step 10,000. The run really went
> from 0-20 ns. Sorry about that, again, I tried to delete the post.
> Anyway, I agree with you that the data from the xvg file is sensible
> and makes me feel better about my simulation. I analyzed the xvg file
> and found that it gives nearly identical values for temperature, Box
> vectors, and density as given by the g_energy summary, but pressure and
> surface tension are off by many orders of magnitude and sometimes sign.
> If you calculate the surface tension using the pressure tensor values
> given by the g_energy summary and the xvg output file, both are
> internally consistent, but do not agree with each other. I understand
> where the data in the xvg file came from because I watched it develop as
> my run progressed. I don't know where the g_energy summary is getting
> those numbers from (or the log file averaging for that matter).
> Here is my g_energy command:
> g_energy -f md.edr -s md.tpr -o energy.xvg -b 19000 -e 20000
> I think I might just write a script file to parse the xvg file from
> g_energy to get me the correct values.
This smells strongly of a bug. The output is all sensible, but the calculated
averages are junk. Please upload a test case to redmine as a new issue so this
can be fixed.
> On Tue, Feb 1, 2011 at 3:31 PM, Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>> wrote:
> Denny Frost wrote:
> This is the 'averages' section
> " <=" ===== ######## ####### ==>
> " <=" === A V E R A G E S ====>
> " <=" = ############ ### ======>
> " St" atistics over 1 0000001 steps u sing 10000001 f rames
> Energies (kJ/mo l)
> Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR)
> 4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00
> Potential Kinetic En. Total Energy Temperature Pressure (bar)
> -9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02
> Box-X Box-Y Box-Z
> 5.47E+00 5.47E+00 5.47E+00
> Total Virial (k J/mol)
> 5.44E+02 -1.30E-01 8.27E-02
> -1.30E-01 5.44E+02 3.46E-02
> 8.27E-02 3.46E-02 5.44E+02
> Pressure (bar)
> 9.96E+02 2.34E-02 -1.51E-02
> 2.34E-02 9.96E+02 -2.77E-02
> -1.51E-02 -2.77E-02 9.96E+02
> Total Dipole (D )
> 0.00E+00 0.00E+00 0.00E+00
> OK, that all looks as expected, except of course the pressure.
> I don't have an RMS section on my log file.
> Is this 4.5.3? It looks like a whole lot of interesting diagnostic
> and other information is now not printed to the .log file that used
> to be. Too bad.
> The final output of the g_energy command is this (for pressure):
> OK, so I'm guessing this isn't complete, but what is really weird is
> that (1) your .mdp file calls for a 5-ns run, but these data are for
> (at least) 10 ns or so and (2) there are multiple data sets, such
> that you're looping back over zero at least twice.
> Strangely, if you analyze just the 0->9990 chunks independently,
> they all give sensible pressures (not quite 1, but +/-7).
> To address point #1: Have you done a continuation with a checkpoint
> file, or are you posting the wrong .mdp file? If you did a
> continuation, are the data in the original 5-ns run sensible? I'm
> wondering if something broke down along the way.
> For #2, what exactly are you passing to g_energy? As in, what
> groups are displayed and what exactly are you choosing?
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
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Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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