On Wed, Jun 04, 2003, Peter Anderson wrote:
>
> Could someone explain briefly the difference between
> using belly and using position restraints when
> performing energy minimizations? Are there situations
> when it's better to use one than the other? Also, are
> there any articles in the literature that discuss
> belly?
Frozen atoms (ibelly=1) never move at all; restrained atoms (ntr=1) can move
more or less, depending upon the value of the force constant in the
restraining potential.
For sander 7, there are few reasons to run frozen atoms, and most simulations
that need to keep things (approximately) fixed should use ntr=1.
..dac
--
==================================================================
David A. Case | e-mail: case.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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Received on Wed Jun 04 2003 - 17:53:02 PDT
