[gmx-users] Inaccurate pressure readings

Denny Frost dsfrost at cableone.net
Tue Feb 1 23:57:52 CET 2011

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.

On Tue, Feb 1, 2011 at 3:31 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> 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
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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