From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 10 2006 - 15:34:12 CST
have you viewed the resulting trajectory in VMD? Do you see anything
unusual happening, like an atom or group flying off? This still sounds
like an issue of a system not being minimized enough or something along
those lines. Also, I'd recommend trying with a timestep of 1 instead of 2.
bo baker wrote:
>I am still stucked by the velocity errors. With the suggestions from
>others, I have modified the '.conf' file: delete the
>'cellBasisVectors', padding my OME grid sizes a bit more; choose
>'useflexsibleCell no'. All these efforts allow the simulation to a bit
>longer, but still stopped premature:
>TIMING: 23500 CPU: 4960.12, 3.24876/step Wall: 5015.77,
>3.28091/step, 109.819 hours remaining, 0 kB of memory in use.
>ENERGY: 23500 16407.7215 10176.8444 1125.4231
>116.4013 -168531.4559 15352.3312 0.0000
>0.0000 42943.8007 -82408.9338 321.8909
>-78444.0002 -78785.3512 308.5296 15004.4553
>119.9913 436736.3972 -5.5312 -3.9712
>ERROR: Atom 1766 velocity is -6825.09 -441.432 -309.29 (limit is 5000)
>ERROR: Atoms moving too fast; simulation has become unstable.
>ERROR: Exiting prematurely.
>WallClock: 5700.964844 CPUTime: 5633.370117 Memory: 0 kB
>I have included my .conf file as an attachment. Thanks for advice.
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