AMBER Archive (2005)

Subject: RE: AMBER: restart file

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Tue Jul 05 2005 - 14:29:27 CDT

I suspect that your system is diffusing too far such that the coordinates no
longer fit in the space allocated in the restrt file. Check the restrt file,
you will probably see lines with ***'s in them. If you are not interested in
measuring diffusion coefficients then you can set IWRAP=1 in your input
file. This will wrap all coordinates back to the central box rather than
tracking the original molecule. This way you shouldn't come accross this
problem.

All the best
Ross

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> Dear helper,
> I run several high temperature simulations (500-600K) with constant
> volume in Amber7, when they reach about 8-9 ns the
> simulations stop and
> messages like the following appear:
> * fmt: read unexpected character
> apparent state: unit 9 named t11.rst
> last format: (6F12.7)
> lately reading sequential formatted external IO
> Abort (core dumped)
> *
> then I tried to run it again using t10.rst, for instant, as
> the restart
> file (and sometimes I changed the interval time of the
> results printed
> in one file). When it comes to use the next restart file, say it
> t11.rst, the same message appear.
> Can someone help me to solve this problem?
> Any help would be appreciated.
>
> Best wishes,
> Harianto.
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