[gmx-users] Inaccurate pressure readings

[Justin A. Lemkul]

Denny Frost wrote:

<snip>

> 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

-- 
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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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