Re: AMBER: neutrality of charge in AMBER 7

From: David A. Case <case.scripps.edu>
Date: Sat, 14 Feb 2004 12:10:22 -0800

On Thu, Feb 12, 2004, Sichun Yang wrote:
>
>
> I just wonder how it works in Amber 7 since ischrgd is removed.
> What is the default? Or I should addions manually?

If the charge is very small (essentially just roundoff error away from
zero) then the charges are adjusted slightly to give exactly zero total
charge.

Otherwise, a neutralizing plasma is used.

....hope this helps...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
==================================================================
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sat Feb 14 2004 - 20:53:00 PST
Custom Search