[gmx-users] Inaccurate pressure readings

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.

-Justin

> 
> 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:
> 
>     <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
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.vt.edu/Pages/Personal/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

========================================