AMBER Archive (2008)

Subject: RE: AMBER: Ewald error estimate

From: Ross Walker (
Date: Thu May 08 2008 - 10:27:15 CDT

> 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,

|\oss Walker

| Assistant Research Professor |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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