Subject: Parallelized SHAKE?

From: [email-masked] (Gabriel Berriz)
Date: Tue, 19 Nov 1996 16:00:41 -0500

Dear netters:

I am trying to find a *published* parallelization of the SHAKE
algorithm.  All I've been able to find is the analytic algorithm
SETTLE of Miyamoto and Kollman, but as far as I can tell, it is only
good for water molecules.  I have also found on the Web various
mentions of parallelized SHAKE routines that are part of recent
versions of CHARMM, AMBER, or GROMOS, but (a) I don't have access to
the source codes, and (b) I find somewhat daunting the idea of poring
through what is surely voluminous code to extract the desired
fragment.  (But maybe it'll come to this... :-/ )

I appreciate any pointers to the literature.

Gabriel Berriz
[email-masked]
Dept. of Chemistry and Chemical Biology
Harvard University

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From: "Dr. Bruno Manunza" <[email-masked]>
Date: Wed, 20 Nov 1996 00:06:27 +0100 (NFT)

> Dept. of Chemistry and Chemical Biology

Gabriel,
	you may found interesting to take a look to the DLPOLY parralel MD 
package at the URL http://gserv1.dl.ac.uk/TCSC/Software/DL_POLY/main.html
The source is freely available (Licence agreement needed)
	The shake algorithm should work with molecules different from water.

bye
Bruno

Dr Bruno Manunza
DISAABA (Dept. of Agricultural Environm. Sci)
University of Sassari
V.le Italia 39
07100 Sassari, ITALY
phone: 39 79 229215
fax:   39 79 229276

e-mail: [email-masked]
e-mail: [email-masked]
e-mail: [email-masked]

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From: [email-masked] (Gabriel Berriz)
Date: Tue, 19 Nov 1996 21:01:56 -0500

Date: Tue, 19 Nov 1996 20:37:26 -0500 (EST)
   From: Rick Venable <[email-masked]>

   A caveat on parallelized SHAKE in CHARMM...

Thank you for the information.

Gabriel Berriz

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From: Rick Venable <[email-masked]>
Date: Tue, 19 Nov 1996 20:37:26 -0500 (EST)

> fragment.  (But maybe it'll come to this... :-/ )

A caveat on parallelized SHAKE in CHARMM-- a SHAKE constraint may not
be imposed across a parallel partition.  For situations when only bonds to
H atoms are constrained, this isn't a problem, since the GROUP structure
defined in the RTF is respected when the parallel partitioning is done.
However, attempting to constrain all bond lengths will lead to problems
for heavy atom to heavy atom bonds that reside in different parallel
partitions (and that will almost always be the case for a macromolecule).

--
Rick Venable                  =====\     |=|    "Eschew Obfuscation"
FDA/CBER Biophysics Lab       |____/     |=|
Bethesda, MD  U.S.A.          |   \  /   |=|  ( Not an official statement or
[email-masked]       \/    |=|    position of the FDA; for that,
http://nmr1.cber.nih.gov/venable.html    |=|    see   http://www.fda.gov  )