Subject: Re: CCL:SHAKE and the MCE.

From: David van der Spoel <[email-masked]>
Date: Sat, 27 Jan 2001 10:41:48 +0100 (CET)

On Fri, 26 Jan 2001, Adam Hixson wrote:

>I just read one of the original accounts of the
>SHAKE algorythm (J Comp Phys 1977 23 327-41),
>and I have a question about the energy produced.
>
>To what extent does a microcannonical ensemble
>simulation using SHAKE conserve the energy?  The
>authors of the above paper mentioned that it
>fluxuated about a stable value, but gave no
>indication as to how great the flux was.
>
>Anybody know anything about this?
Energy conservation is very good, but probably not quite as good as when
using normal potentials like harmonic bonds etc. because you still have to
use a numerical solution for the constraint equations. You can usually set
a tolerance that determines how good the convergence should be, but lower
tolerance means higher computational cost. It is worth mentioning that
there is also a "follow up" algorithm to shake that is non iterative:
@article{Hess97,
  author = 	 {B. Hess and H. Bekker and H. J. C. Berendsen and
                  J. G. E. M. Fraaije},
  title = 	 {{LINCS}: A Linear Constraint Solver for Molecular Simulations},
  journal = 	 "J. Comp. CHem.",
  year = 	 1997,
  volume =       18,
  pages =        {1463--1472}
}

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel		Biomedical center, Dept. of Biochemistry
s-mail:	Husargatan 3, Box 576,  75123 Uppsala, Sweden
e-mail: [email-masked]	www: http://zorn.bmc.uu.se/~spoel
phone:	46 18 471 4205		fax: 46 18 511 755
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