From chemistry-request@ccl.net Mon Sep 16 05:12:47 1991
Date:         Mon, 16 Sep 91 10:48:54 CST
From: Wolfram Koch <KOCHW%DHDIBM1.BITNET@OHSTVMA.ACS.OHIO-STATE.EDU>
Subject:      Xenon AO basis set
To: "comp. chem. list" <CHEMISTRY@ccl.net>
Status: R

Hi,
I am looking for a good GTO basis set for Xe (no pseudeopotential!)
Should be flexible enough to give reasonably good
polarizibilities.
I'd appreciate any help and suggestions.

Thanks.

Wolfram Koch

Institute for Supercomputing and Applied Mathematics
IBM Heidelberg Scientific Center
D-6900 Heidelberg, Germany
FAX: +49 6221 404-296
e-mail: KOCHW@DHDIBM1.BITNET

From chemistry-request@ccl.net Mon Sep 16 05:16:16 1991
Date: Mon, 16 Sep 91 11:04:02 +0200
From: Florian Mueller-Plathe <fmp@igc.ethz.ch>
To: CHEMISTRY@ccl.net
Subject: Parallel MD
Status: R

Hi there,
I received about a dozen notes reading somethink like: "I am not
the person who originally requested information about parallel MD
but I would appreciate if you could send me a copy of your list of
references as well." Well, here it is. I am posting it to the list
Please have mercy and do not send in more requests!
The list contains most of the refences on parallelisation I know.
It is probably still incomplete. Send in your favourite refs and I
will add them to the list. There are also a few references on vector-
isation which are in the list for historical reasons.
Cheers,
Florian Mueller-Plathe (fmp@igc.ethz.ch)


%A D Fincham
%A B J Ralston
%T Molecular dynamics simulation using the Cray-1 vector processor
%J Comput. Phys. Commun.
%V 23
%P 127-134
%D 1981

%A R Vogelsang
%A M Schoen
%A C Hoheisel
%T Vectorisation of molecular dynamics Fortran programs using the Cyber 205 vector processing computer
%J Comput. Phys. Commun.
%V 30
%P 235-241
%D 1983

%A F Sullivan
%A R D Mountain
%A J O'Connel
%T J. Comput. Phys.
%J J. Comput. Phys.
%V 5
%P 272-279
%D 1984

%A S Brode
%A R Ahlrichs
%T An optimised MD program for the vector computer cyber 205
%J Comput. Phys. Commun.
%V 42
%P 51-57
%D 1986

%A W F van Gunsteren
%A H J C Berendsen
%A F Colonna
%A D Perahia
%A J P Hollenberg
%A D Lellouch
%T On searching neighbours in computer simulations of macromolecular systems
%J J. Comput. Chem.
%V 5
%P 272-279
%D 1984
%X 

%A J Boris
%T A vectorized neighbours algorithm of order N using a monotonic logical grid
%J J. Comput. Phys.
%V 66
%P 1-20
%D 1986

%A O Teleman
%A B Jonsson
%T Vectorizing a general-purpose molecular dynamics simulation program
%J J. Comput. Chem.
%V 7
%P 58-66
%D 1986

%A G S Grest
%A B Duenweg
%A K Kremer
%T Vectorized link-cell all Fortran code for molecular dynamics simulations for a large number of particles
%J Comput. Phys. Commun.
%V 55
%P 269-285
%D 1989

%A A Windemuth
%A K Schulten
%T Molecular dynamics simulation on the Connection Machine
%J Molec. Simul.
%V 5
%P 353-361
%D 1991

%A T W Clark
%A J A McCammon
%T Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architecture
%J Computers and Chemistry
%V 14
%P 219-224
%D 1990

%A R D Skeel
%T Macromolecular dynamics on a shared-memory multiprocessor
%J J. Comp. Chem.
%V 12
%P 175-179
%D 1991

%A M R S Pinches
%A D J Tildesley
%A W Smith
%T Large scale molecular dynamics on parallel computers using the link-cell algorithm
%J Molec. Simul.`
%V 6
%P 51-87
%D 1991

%A D Fincham
%T Parallel computers and molecular simulation
%J Molec. Simul.
%V 1
%P 1-45
%D 1987

%A F Bruge
%A V Martorana
%A S L Fornili
%T Concurrent molecular dynamics simulation of ST2 water on a Transputer array
%J Molec. Simul.
%V 1
%P 309-320
%D 1988

%A A R C Raine
%A D Fincham
%A W Smith
%T Systolic loop methods for molecular dynamics simulation using multiple Transputers
%J Comput. Phys. Commun.
%V 55
%P 13-30
%D 1989

%A  H G Petersen
%A J W Perram
%T Molecular dynamics on transputer arrays I. Algorithm design, programming issues, timing experiments and scaling projections
%J Mol. Phys.
%V 67
%P 849-860
%D 1989

%A H Heller
%A H Grubmueller
%A K Schulten
%T Molecular dynamics simulation on a parallel computer
%J Molec. Simul.
%V 5
%P 133-165
%D 1990

%A S J Zara
%A D Nicholson
%T Grand canonical ensemble Monte Carlo simulation on a Transputer Array
%J Molec. Simul.
%V 5
%P 245-261
%D 1990

%A W Smith
%T Molecular Dynamics on hypercube parallel computers
%J Comput. Phys. Commun.
%V 62
%P 229-248
%D 1991

%A C J Craven
%A G S Pawley
%T Molecular dynamics of rigid polyatomic molecules on transputer arrays
%J Comput. Phys. Commun.
%V 62
%P 169-178
%D 1991
%X 

%A F Mueller-Plathe
%T Parallelising a molecular dynamics algorithm on a multi-processor workstation
%J Comput. Phys. Commun.
%V 61
%P 285-293
%D 1990

%A F Mueller-Plathe
%A D Brown
%T Multi-colour algorithms in molecular simulation: vectorisation and parallelisation of internal forces and constraints
%J Comput. Phys. Commun.
%V 64
%P 7-14
%D 1991

%A M Schoen
%T Structure of a simple molecular dynamics Fortran program optimized for Cray vector processing computers
%J Comput. Phys. Commun.
%V 52
%P 175-185
%D 1989

%A S Gupta
%T Vectorization of molecular dynamics simulation for fluids of nonspherical molecules
%J Comput. Phys. Commun.
%V 48
%P 197-206
%D 198
%D 1988

%A T P Straatsma
%A J A McCammon
%T ARGOS, a vectorized general molecular dynamics program
%J J. Comp. Chem.
%V 11
%P 943-951
%D 1990

%A Z A Rycerz
%T Acceleration of molecular dynamics simulation of order N with neighbour list
%J Comput. Phys. Commun.
%V 60
%P 297-303
%D 1990

%A F Bruge
%A S L Fornili
%T A distributed dynamic load balancer and its implementation on multi-transputer systems for molecular dynamics simulation
%J Comput. Phys. Commun.
%V 60
%P 39-45
%D 1990

%A F Bruge
%A S L Fornili
%T Concurrent molecular dynamics simulation of spinodal phase transition on transputer arrays
%J Comput. Phys. Commun.
%V 60
%P 31-38
%D 1990

%A L J Alvarez
%A A Alavi
%A J I Siepmann
%T A vectorisable algorithm for calculating three-body interactions
%J Comput. Phys. Commun.
%V 62
%P 179-186
%D 1991

%A D C Rapaport
%T Multi-million particle molecular dynamics I. Design considerations for vector processing
%J Comput. Phys. Commun.
%V 62
%P 198-216
%D 1991

%A D C Rapaport
%T  Multi-million particle molecular dynamics II. Design considerations for parallel processing
%J  Comput. Phys. Commun.
%V 62
%P 217-228
%D 1991

%A K Refson
%A G S Pawley
%T Correlations in the plastic crystal phase of n-butane
%J Comput. Phys. Commun.
%V 62
%P 279-288
%D 1991

%A S Chynoweth
%A U C Klomp
%A L E Scales
%T Simulation of organic liquids using pseudo-pairwise interatomic forces on a toroidal transputer array
%J Comput. Phys. Commun.
%V 62
%P 297-306
%D 1991

%A D Fincham
%A P J Mitchell
%T Multicomputer molecular dynamics simulation using distributed neighbour lists
%J Molec. Simul.
%V (submitted)
%O also Daresbury Preprint DL/SCI/P730T, 1990

%A V Yip
%A R Elber
%T Calculations of a list of neighbors in molecular dynamics simulations
%J J. Comp. Chem.
%V 10
%P 921-927
%D 1989

%A D W Noid
%A B G Sumpter
%A B Wunderlich
%A G A Pfeffer
%T Molecular dynamics simulations of polymers: methods for optimal Fortran programming
%J J. Comp. Chem.
%V 11
%P 236-241
%D 1990

%A D C Rapaport
%T Large-scale molecular dynamics simulation using vector and parallel computers
%J Comput. Phys. Rep.
%V 9
%P 1-54
%D 1988

%A A R C Raine
%T Systolic Loop Methods for Molecular Dynamics Simulation, Generalised for Macromolecules
%J Mol. Sim.
%V 7
%P 59-69
%D 1991

%A H Grubmueller
%A H Heller
%A A Windemuth
%A K Schulten
%T Generalized Verlet Algorithm for Eficient Molecular Dynamics
Simulations with Long-range Interactions
%J Mol. Sim.
%V 6
%P 121-142
%D 1991

%A S J Zara
%A D Nicholson
%T Grand Canonical Ensemble Monte Carlo Simulation on a
Transputer Array
%J Mol. Sim.
%V 5
%P 245-261
%D 1990

From chemistry-request@ccl.net Mon Sep 16 12:45:43 1991
Date: Mon, 16 Sep 91 11:29:42 CDT
From: heller@lisboa.ks.uiuc.edu (Helmut Heller)
To: Florian Mueller-Plathe <fmp@igc.ethz.ch>
Subject: Re: Parallel MD
Status: R

Hello Florian,

Thanks for posting your list on parallel MD. I have a few other articles  
which you might want to add for further reference:

@inproceedings{BOEH90,
author={Klaus Boehncke and Helmut Heller and Helmut Grubm\"uller and Klaus  
Schulten},
title={Molecular Dynamics Simulations on a Systolic Ring of Transputers},
booktitle={Transputer Research and Applications~3},
organization={North American Transputer Users Group},
editor={Alan S. Wagner},
publisher={{IOS} Press},
pages={83--94},
year={1990},
  address={Amsterdam},
annotes={Proceedings of the Third Conference of the North American Transputer  
Users Group, April~26--27, 1990 --- Sunnyvale, CA}
}

@inproceedings{SCHU91,
  author={Klaus Schulten},
  title={Computational Biology on Massively Parallel Machines},
  booktitle={Proceedings of the
International Conference on Parallel Computation, Salzburg, Austria},
  publisher={Springer, New York},
  year=1991,
  note={in press}
}

@inproceedings{LEAT91,
  author={Leathrum, Jr., James F.  and Board, Jr., John A. },
  title={Parallelization of the Fast Multipole Algorithm using the {B012}  
Transputer Network},
  booktitle={{TRANSPUTING91}},
  year=1991,
  editor={Dyke Stiles and Tosiyasu L. Kunii and Andr\'{e} Bakkers},
  pages={296--310},
  volume=1
}

@inproceedings{BOAR90,
  author={Board, Jr., John A.   and Leathrum, Jr., James F.},
  title={The Fast Multipole Algorithm on Transputer Networks},
  booktitle={{NATUG~3:} Transputer Research and Applications~3},
  year=1990,
  editor={Alan S. Wagner},
  pages={63--74}
}

@article{GREE87,
  author={L. Greengard and V. Rohklin},
  title={A Fast Algorithm for Particle Simulation},
  journal=JCMP,
  volume=73,
  pages={325--348},
  year=1987
}
Cheers, Helmut  (W9/DH0MAD) _________________________________________________
heller@lisboa.ks.uiuc.edu   "Knowledge must be gathered and cannot be given" 

u27013@ncsagate.bitnet                   ZEN, one of BLAKES7                

Phone: (217)244-1586, FAX: (217)244-2909 ------------------------------------
Helmut Heller, University of Illinois at Urbana-Champaign, Beckman Institute
Theoretical Biophysics Group, Transputer Lab, Room 3151, MC 251
405 N. Mathews Ave., Urbana, IL 61801, U.S.A.