On Tue, Oct 31, 2000, Marios Philippopoulos wrote:
> I could be wrong about this but I think that Ewald sums are turned on by default
> in AMBER6. I don't know if there is a way to turm them off. Is there such a
> parameter
> to be set in AMBER6?
>
> If not, I am also at a loss how one can perform vaccum simulations.
Turning off periodicity (setting ntb=0) also turns off PME, since PME
depends upon having a periodic system.
With ntb=0, you need to set igb to 1,2 or 3 (depending upon what you want).
With igb=2 or 3, you will get a "vacuum" simulation.
However, sander in version 6 is not well optimized for vacuum simulations.
While we don't necessarily recommend vacuum simulations (this is almost
the 21st century....), it is generally more efficient to use sander_classic
than sander for this sort of calculation.
...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 Oct 31 2000 - 10:55:15 PST
