AMBER Archive (2000)

Subject: gb/sa

From: Cui Guanglei (cuigl_at_morita.chem.sunysb.edu)
Date: Thu Apr 13 2000 - 10:17:32 CDT

Dear Amber Users,
    I have a question about GB/SA simulation. I see the bench.out in
$amber/test/gb_rna directory. It has parameter 'saltcon', which is not
listed in the manual. Is this equivalent to putting counterions around
rna? If yes, how should the concentration be determined? Is it dependent
of the charges of rna? What could be the problem by using explicit
counterions?
    Another question is about the cutoff. What will be the proper value
for cut in GB/SA simulation? I see 99 is used in that test.
    Thanks in advance. 

-- 
Guanglei Cui
State University of New York
Department of Chemistry
Stony Brook, 11794-3400