AMBER Archive (2002)

Subject: Re: How to decrease the solvated system in Amber6?

From: David A. Case (case_at_scripps.edu)
Date: Tue Jul 02 2002 - 06:38:50 CDT

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
==================================================================