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 consistent:
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? -- View this message in context: http://gromacs.5086.n6.nabble.com/g-energy-menu-choices-inconsistent-tp5001494.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists