RE: amber-developers: RGBMAX=25A by default?

From: Yong Duan <>
Date: Thu, 21 Apr 2005 20:52:44 -0700

I also add that GB/PB are practically the only choices in many cases
(protein structure scoring, constant pH, etc). Energies from explicit
water simulations are not going to be helpful at all in these things.

I did not mean to comment on a recent post. What happened was that two
of my people noticed slow GB performance (to the point that they started
ask me why I insisted GB). Initially, I thought something funny in their
systems. Then, I looked at their output files and noticed more than 80%
of time was spent on diag terms and realized the default rgbmax. I did
not mean at all to say that GB is less efficient than PME (of course
not). What I meant was that if we have a set of realistic default
parameters the users could be even more impressed with GB :). By the
way, improvement in efficiency (e.g., nonbonded list) can also help. All
these take time and effort!!


4. Don't forget that GB explores conformational space a lot faster than
explicit solvent simulations do. The difference can be an order of
magnitude, and should be taken into consideration for some types of

Received on Wed Apr 05 2006 - 23:49:57 PDT
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