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 <[email protected]
<mailto:[email protected]>> 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
========================================
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