[gmx-users] RE : long-term drift and crash

Mark Abraham Mark.Abraham at anu.edu.au
Thu Aug 23 06:22:16 CEST 2007

BON Michael wrote:
> Hi,
> Sorry fot no answering accurately.
> Here is new insight for understanding my problem.
> In fact, even simulations of pure water (tip4p and tip4p_ew) don't work !
> And those simulations crash with a strange periodic pattern : still using g_msd, I observe
> on the msd plot sudden jumps that occur exactly every 10.000 ps ! By "jump" I mean a violent
> increase of the slope of the curve that lasts a short time, which is exactly 0.1 ps each time in my case. The curve is linear with the correct diffusion constant otherwise. I observe such jumps between 10.0 and 10.1 ps, 20 and 20.1 ps 30 and 30.1 ps, and so on, and each time the jumps have a higher magnitude than the previous one, till the simulation crashes.

Are you running this job continuously? The simplest explanation I can 
think of for this phenomenon would be restarting with regeneration of 
velocities, or a mismatch of coordinates and velocities... but if your 
simulation is not being restarted this is impossible.

Otherwise, this problem is bewildering.

How large is your system?
What gromacs version are you running? What hardware? What configure 
flags were used?


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