AMBER Archive (2003)

Subject: Re: ibelly and ntr

From: sychen (yuann_at_bioinfo.ndhu.edu.tw)
Date: Tue Apr 15 2003 - 22:03:57 CDT

Dear Author,
  Is there any reference about the difference between belly simulation
and position restrain? I'd like to know about the function if them, and
I don't know why belly is not recommended with EWALD subroutine.

Thank you!

Best Regards,

sychen

On Tue, 15 Apr 2003 16:13:11 -0700
"David A. Case" <case_at_scripps.edu> wrote:

> On Tue, Apr 15, 2003, Youyi Peng wrote:
>
> > I can't really understand the differnece between ibelly=1 and ntr=1,
> > both for frozen /restrained atoms...
>
> ibelly=1 are *con*straints: the frozen atoms cannot move at all.
>
> ntr=1 are *re*straints: the restrained atoms can move, but won't move far;
> how far depends on the size of the force constant you use.
>
> I'd recommend restraints to keep the backbone (nearly) fixed, but there is
> no fundamental reason not to use constraints...
>
> ..good luck...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
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> La Jolla CA 92037 USA | http://www.scripps.edu/case
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