On Mon, Jul 01, 2002, Ling Zhang wrote:
>
> I tried to decrease my solvated system by using a trucated octahedral
> box in Leap of Amber6. But the result is still not satifactory. Could
> you give me some suggestions in decreaseing the system without
> affecting the quality of the simulation? Thanks a lot.
Without knowing how big your box was, or what was "not satisfactory", it
is hard to give much advice. Here is the LEaP command I usually use:
solvateOct x WATBOX216 12.0 0.75
You could compare that to what you use. Note that I have never simulated
something as large as a 900 residue protein in water (nor have many other
people, I imagine): you are trying something rather difficult, and should
expect things to require lots of computer time and patience.
..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 Jul 02 2002 - 04:38:50 PDT
