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. <div>
<br></div><div>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).</div>
<div><br></div><div>Here is my g_energy command:</div><div><br></div><div>g_energy -f md.edr -s md.tpr -o energy.xvg -b 19000 -e 20000</div><div><br></div><div>I think I might just write a script file to parse the xvg file from g_energy to get me the correct values. <br>
<br><div class="gmail_quote"><br></div><div class="gmail_quote">On Tue, Feb 1, 2011 at 3:31 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<br>
<br>
Denny Frost wrote:<br>
<br>
<snip><div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
This is the 'averages' section<br>
<br>
" <=" ===== ######## ####### ==><br>
" <=" === A V E R A G E S ====><br>
" <=" = ############ ### ======><br>
" St" atistics over 1 0000001 steps u sing 10000001 f rames<br>
Energies (kJ/mo l)<br>
Bond Angle Ry ckaert-Bell. LJ (SR) Coulomb (SR)<br>
4.57E+03 3.62E+03 3.34E+03 -2.08E+04 0.00E+00<br>
Potential Kinetic En. Total Energy Temperature Pressure (bar)<br>
-9.28E+03 1.63E+04 7.05E+03 3.00E+02 9.96E+02<br>
Box-X Box-Y Box-Z<br>
5.47E+00 5.47E+00 5.47E+00<br>
Total Virial (k J/mol)<br>
5.44E+02 -1.30E-01 8.27E-02<br>
-1.30E-01 5.44E+02 3.46E-02<br>
8.27E-02 3.46E-02 5.44E+02<br>
Pressure (bar)<br>
9.96E+02 2.34E-02 -1.51E-02<br>
2.34E-02 9.96E+02 -2.77E-02<br>
-1.51E-02 -2.77E-02 9.96E+02<br>
Total Dipole (D )<br>
0.00E+00 0.00E+00 0.00E+00<br>
<br>
</blockquote>
<br></div>
OK, that all looks as expected, except of course the pressure.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I don't have an RMS section on my log file.<br>
</blockquote>
<br></div>
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.<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
The final output of the g_energy command is this (for pressure):<br>
</blockquote>
<br>
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.<br>
<br>
Strangely, if you analyze just the 0->9990 chunks independently, they all give sensible pressures (not quite 1, but +/-7).<br>
<br>
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.<br>
<br>
For #2, what exactly are you passing to g_energy? As in, what groups are displayed and what exactly are you choosing?<br><font color="#888888">
<br>
-Justin</font><div><div></div><div class="h5"><br>
<br>
-- <br>
========================================<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
========================================<br>
-- <br>
gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a><br>
<a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target="_blank">http://lists.gromacs.org/mailman/listinfo/gmx-users</a><br>
Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target="_blank">http://www.gromacs.org/Support/Mailing_Lists/Search</a> before posting!<br>
Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target="_blank">gmx-users-request@gromacs.org</a>.<br>
Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target="_blank">http://www.gromacs.org/Support/Mailing_Lists</a><br>
</div></div></blockquote></div><br></div>