> I guess maybe the problem caused by high VDW, but not sure. I try lots of
> methods such as run short MD with shorter time steps (0.5fs or 1fs), but
> the same problem happens. Maybe my initial structure builded by nucgen has
> a serious problem, but I can not find the reason.
Can you explain what you mean by serious problem and then perhaps we can try
and help.
I would suggest running MD starting at 0K with no thermostat and NVE. Set
nstlim = 500, set ntwx=1 and dt=0.0005. Then run the simulation and you'll
get a frame in the trajectory file every half a femtosecond. You can then
visualize this in something like VMD and you will be able to see where any
problems such as blowing up originate from.
Good luck,
Ross
/\
\/
|\oss Walker
| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk | PGP Key available on request |
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Received on Sun May 11 2008 - 06:07:30 PDT
