[gmx-users] why the trajectory file is not output

Mark Abraham Mark.Abraham at anu.edu.au
Fri Jan 23 22:41:20 CET 2009

He, Yang wrote:
> Hi Mark,
> I just choose a small number of steps but it also does not work.it always shows that
> starting mdrun 'MODEL CYLINDER'
> 10000 steps,    300.0 ps.
> Segmentation fault (core dumped)

OK, so that's a generic error message suggesting something is severely 
wrong. Check the end of your .log file, but probably you've got 
something badly wrong with your machine or installation. GROMACS is not 
in the habit of doing inexplicable segmentation faults under normal 
operating systems.

Your use of thermostats is inadvisable, see 

Your use of applied electric fields is abnormal - when trying to 
diagnose a problem, you should simplify in small, discrete steps until 
something works, so that you learn where the problem is being caused.


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