On Tue, Nov 12, 2002, Kristina Furse wrote:
> >Setting ntb=1 implies you have a periodic simulation, not a vacuum. My
> >recollection was that we also recommended using sander_classic for vacuum
> >calculations in Amber 6. You can get things to work in sander (check the
> >instructions or the mail archives carefully), but this was less efficient
> >than running the calculation with sander_classic.
>
> Does the same hold true for sander in Amber 7? Would it be better to continue
> using sander_classic in Amber 6 for vacuum calculations?
>
Sander7 should be nearly as good as sander_classic (amber6) for vacuum
simulations. However, there is no particular reason to change (for most
types of studies) if you are satisfied with sander_classic.
..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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Received on Tue Nov 12 2002 - 15:16:52 PST
