[gmx-users] g_energy menu choices inconsistent?

Ladasky blind.watchmaker at yahoo.com
Tue Oct 2 07:40:31 CEST 2012

I have been trying to automate my simulation setup and monitoring.  I wrote a
script which calls g_energy, and automatically generates plots of potential
energy from my EM step, temperature from my NVT equilibration step, and
pressure and density from my NPT equilibration step.  For each of these
three simulations, it appeared that the numbering on the g_energy menu was

Potential = 11, Temperature = 15, Pressure = 16, Density = 22.

I wrote my program assuming that these numbers would always describe the
parameters listed.  Maybe not?

Something is still going wrong with my production run, I'm getting a
segmentation fault after about 40,000 steps (sigh, I almost thought I had
this whole setup understood and debugged).  So I used my graphing program to
check the temperature, and the results were... odd, bouncing from +300 to
-100.  The values in my MD.log file disagreed with my graph, they were all
within a few degrees of 310K, my target temperature.

So I re-ran g_energy directly, bypassing my program, using my production-run
ener.edr file as input.  The menu showed:

Potential = 10, Temperature = 13, Pressure = 15, Density = 21.

Seeing this number shift, I understand why my "temperature" graph for the
production looked wrong -- I was actually graphing pressure.

Not knowing what menu options to expect will impair my ability to automate
the running of g_energy.  I can try some tricks to capture that menu each
time I run the program, but it will be a chore.

I would also like to understand: what is the REASON that these numbers might
change between runs?

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