[gmx-users] Inaccurate pressure readings
Justin A. Lemkul
jalemkul at vt.edu
Tue Feb 1 23:31:16 CET 2011
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
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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