Re: virtual box

From: David A. Case <>
Date: Tue 7 Jan 2003 15:56:29 -0800

On Tue, Jan 07, 2003, eric hu wrote:

> Hi I'm running md with NMR bond restraints. Amber 7
> stops after 14ps with the following message.

> The system has extended beyond
> the extent of the virtual box.

You should look at what your system is doing: it is apparently changing
shape (expanding) very quickly (with 14-35 ps) by a large amount. If
this is not what it "should" be doing, then you need to figure out why
that is happening.

If you have a simulation that for some reason needs to change the size
of the molecule by a very large amount, you can modify "extraboxdim" in
nonper.h. This variable is the buffer around the intial structure, and
can be made bigger, but be sure that is really the problem.

> &wt type='REST', istep1=0,istep2=0,value1=1.0,
> value2=1.0,

I hope you understand that the above weight change doesn't do anything,
since the default value is 1.0 anyway.

> r1=0.00000E+00,r2=2.130,r3=2.130,r4=5.00,
> rk2=9999.0,rk3=9999.0,

These are quite unreasonable force constants (rk2,rk3): try a value something
like a thousand times smaller. I'm actually somewhat surprised that the
simulation runs at all with that sort of NMR restraint....

..hope this helps...dac

David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |
Received on Tue Jan 07 2003 - 15:56:29 PST
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