From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Jan 10 2006 - 15:34:12 CST
Dear Bo,
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.
Peter
bo baker wrote:
>Hello, NAMD:
>
>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
>Program finished.
>
>
>I have included my .conf file as an attachment. Thanks for advice.
>
>
>Bo
>
>
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