AMBER Archive (2003)

Subject: Re: virtual box

From: eric hu (erichu_linux_at_yahoo.com)
Date: Wed Jan 08 2003 - 01:35:09 CST

The reason I use big force constant is because I do
not want the bond length to change at all during the
simulation. The system does change quite a bit. Thank
you for your suggestion.

Eric
--- "David A. Case" <case_at_scripps.edu> wrote:
> 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:
> case_at_scripps.edu
> 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 |
> http://www.scripps.edu/case
>
==================================================================
>

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