AMBER Archive (2004)

Subject: AMBER: Amber 8 - Energy Minimization Parameters

From: Nhat-hang Duong (nhduong_at_rci.rutgers.edu)
Date: Wed Aug 25 2004 - 10:34:28 CDT

Hi all,

I'd like to ask for clarification in setting the parameters for the energy
minimization step (using implicit solvent):

In the manual (p. 102) the default for MAXCYC is 1. Does it mean that if
I set it at 1, the system will keep running until it reaches the
closet local minimum? Does this also mean that one has no control nor
prediction over how long this minimizing process will go?

Another related issue is that: in the tutorial (DNA - an excellent
tutoria!), the suggested, trial value for MAXCYC is 500. This allows the
program to perform 500 nstep (which I guess corresponds to some number of
cycles); and the program stops when it reaches the nstep of 500. Is this
value contradicted with the default value of 1?

Thanks for any help in advance,
--Hang

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