[gmx-users] energy debugging

[Anton Feenstra]

Hi,


I'm trying to debug a 'nan' total energy for a large system (protein,
bilayer, ligand and water, >120k atoms). I'd like to know which of
the energy components are responsible. It used to be possible to get
detailed output by setting
nstenergy = 1
nstlog    = 1
energy_grps = Protein DMP HIM Sol
and 'setenv LOG_BUFS 0' to turn off ouput file buffering. However,
mdrun now refuses to print any energy group information in the log
file (even with -nocompact), and the enrgy file refuses to be filled
(it remains empty). Since the system is pretty large, we don't feel
like waiting for the buffers to flush (if they ever will).

Any help, or suggestions?

-- 
Groetjes,

Anton
  ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
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