Re: amber-developers: Block of ice

From: Thomas E. Cheatham, III <>
Date: Mon, 11 Apr 2005 10:25:10 -0700

> I thought Berendsen's scaling makes "block of ice". But we have gone
> back to single-scaling (vs separate solvent/solute scaling) since AMBER
> 6/7? Any of you observed the "block of ice" thing again? Any
> explanation?

Single-scaling (or in fact *any* scaling; see Harvey et al), especially if
there is not -complete- energy conservation will over time lead to this
behavior. Sources of incomplete energy conservation in AMBER include
cutoff, constant pressure, SHAKE tolerances that are not very low, time
step, ... It is highly recommended that center of mass motion be removed
"often" where often is a debatable quantity ranging from at every step to
every half ns or so depending on how large an energy drain/artifact.

For a greater discussion, see:

Harvey et al. JCC 19, 726-740 (1998) [better discussion/derivation]
Chiu et al. JCC 21, 121-131 (2000)

Received on Wed Apr 05 2006 - 23:49:58 PDT
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