EMERSON CENTER a Publication of the Cherry L

EMERSON CENTER A Publication of the Cherry L. Emerson Center for Scientific Computation http://www.emerson.emory.edu

Volume 1, March 15, 1998

HIGH-END COMPUTATIONAL FACILITY

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FOR YOUR SERVICE

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The Cherry L. Emerson Center for Scientific Computation may not be the

best known center on campus, but it surely is one of the most active scientific

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research facilities. The Emerson Center was estab-

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lished in 1991, with a generous gift of Emory Alum-

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¦%8j¤¤ @Pp>¤<¤%<> @¤P¤¤ nus, Cherry L. Emerson, and has a dual mission to

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computational chemistry and physics, and to provide

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a high-end of computational services to the Emory

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research community. It presently owns and operates an IBM9076 SP2 parallel computer with 14 proces-

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sors, as well as fifteen IBM, HP and SGI worksta-

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tions. It also offers a variety of application software

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✾ Ô Õ¦Õ×Ö«Ø and consulting services in computational chemistry

Õ-ç/èàé and physics, in addition to basic mathematical and

graphic libraries. With the use of its facility, the Cen- Mr. Cherry L. Emerson

êjêëêëêëêëêjêëêìê ter subscribers have published over 200 scientific papers in the first six years of

existence, and have put the name of Emory clearly on the map of computational

chemistry and physics.

We are currently ex-

panding the scope of the

FREE-TRIAL Center to other disciplines, including computational SUBSCRIPTION!

chemical, physical and bio-

If you are not sure whether you logical sciences, and to en- may benefit from the Emerson compass a much broader Center services and facilities, you

may now try the service (hard- base of scientific comput-

ware, software and consulting) ing. This newsletter is one FREE for 3 months! It is the of our efforts to reach out newest feature initiated by the

recent Emerson Center Executive to potential users who

Committee meeting in an effort might need the Center’s to reach out to the university com- Prof. Keiji Morokuma, Director, Emerson Center computing hardware, soft- munity. Please call the Emerson

ware and consulting services for their research. Through issues of this newsletter Center at 727-2380 or email

[email protected] we plan to provide up-to-date information about the Center and its facilities and for details. Also, please make activities.

sure you return the enclosed

USER SURVEY form for future If you have a need for high-end computing for your research, please contact

information updates.

the Emerson Center. The Center is easy to reach, via internet web page, e-mail, telephone or visit, whichever is convenient to you. © 1998-99 VISITING FELLOWSHIP Meet the Emerson © © The Emerson Center offers visiting fellowships in computational chemistry/physics © throughout the year. Scientists from academic institutions all over the world who want Center Staff: © © to perform intensive research in computational chemistry/physics for one to several

í/îXïPðòñ¨ó<ô is still available for visiting fellows interested in collaborating with scientists doing

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■ © Collaborator: Prof. J. M. Bowman, Chemistry ©

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■ © Dr. Harold Basch

Univ. of Reading, UK Ã ©

Ã Bar-Ilan Univ., Israel

Hampden-Sydney College, VA Ã ©

Ã Univ. of Reading, UK

Ã © Eötvös University, Hungary

Ã Eötvös University, Hungary

Nagoya University, Japan Ã

Bogolinbov Inst., Ukraine

Ã ©

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Univ. of S. California, CA Ã

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Hong Kong Univ., Hong Kong

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£-./ (¡§#¢4/£ Dr. Shogo Sakai ©

■ © Dr. Tamar Seideman ©

© Nat. Res. Council, Canada 2 The Emerson Center Subscribers The Center is supported, in part, by “subscribers” or faculty members who purchase shares in order to gain access to its resources for their research projects. IBM workstations are housed in their labs while controlled by the LoadLeveler queu- ing system. Currently, there are nine subscribers, eight from the chemistry department and one from physics. In addition, there is a Chemistry departmental subscription, providing access to the Emerson Center for class use and occasional users

in the department. The following is a list of faculty subscribers and their research interests

Ä â â

Joel Bowman (Phys. Chemistry) Ä Keiji Morokuma (Phys. Chemistry)

Ä â â

(404) 727-6592 Ä (404) 727-2180 â

[email protected] Ä [email protected]

Ä â â

Quantum Calculations of Chemical Ä Quantum Chemical Studies of Chemical â

Reaction Dynamics and Vibrations of Ä Reaction Mechanisms: Transition

Ä â â

Large Molecules Ä States for Gas Phase Reactions, â

Ä Organic Reactions, Organometallic â

Fereydoon Family (Physics) Ä â

Ä Reactions and Enzymatic Reactions â

(404) 727-4293 Ä â

[email protected] Ä

Ä â â

Monte Carlo Simulation and Molecular Ä â

Dynamics of Models of Material Ä

Ä â â

Growth and Other Non-equilibrium Ä

Ä â

Phenomena Å/ÆÈÇ£ÉFÊ ËiÌÎÍ©Ï>Å¯Ð¬ÌÑÅ/Ê§Ç ËiÒÔÓÕÅÖÒ×Í¥Å/Ê

Ä â

Karl Hagen (Inorg. Chemistry) ÐÙØ>Å/Ú4Û×Í©ÜÞÝ#Å8Ó¯ËiÌÑÌÑÜÞÍ©Í¥Å/ÅÙßàÅ/Å/Í©ÜÞÒ§á

Ä â â

(404) 727-6556 Ä â

[email protected] Ä Designed Mimic of the Breast The newly formed Emerson Center Execu- â

Ä Cancer Agent Taxol tive Committee (ECEC) had their first â Structural Studies of Supramolecular Ä

Contributed by Dennis Liotta & Jim Snyder â

Model Complexes as Models of Ä meeting on Feb. 9, 1998. The committee, â

Ä appointed by the Provost, consists of three â

Metalloproteins Ä â

Ä faculty members: Keith Wilkinson (Bio- â

Ä Dennis Liotta (Org. Chemistry) chemistry), Michael Heaven (Chemistry),

â Michael Heaven (Phys. Chemistry) Ä

(404) 727-6602 and Al Padwa (Chemistry-will join in fall), â

(404) 727-6617 Ä â

Ä [email protected] and is chaired by Keiji Morokuma, Direc- â [email protected] Ä

Computational Approaches for Examin- tor of the Emerson Center. It will oversee â

Calculation of Potential Energy Ä â

Ä ing Enzyme/Ligand Interactions; Ab all matters related to administrative sup- â Surfaces for Weakly Bound Systems Ä

Initio Calculations for Assisting port and operation. At its first meeting, â

Ä Morokuma reported to the committee on â

M.C. Lin (Phys. Chemistry) Ä Synthetic Strategies and/or gaining â

Ä the current status of the Emerson Center â

(404) 727-2825 Ä Understanding of Synthetic Results; and its operations. Technical issues re- â

[email protected] Ä Effective Core Potentials for Examining lated to hardware and software upgrades

Ä â â

Calculation of Potential Energy Ä the Electrostatics of Ligands Containing were discussed. The committee also re- â

Surfaces for Combustion Related Ä Metals viewed applications for the 1998/99

Ä â â

Reactions and Reactions on Solid Ä Emerson Center Fellowship, and selected â

Surfaces Ä Fred Menger (Org. Chemistry) 6 award winners. (See page 2 of this news- â

Ä (404) 727-6599 letter for names of award winners.) Addi-

Ä â â

Ä Optimization of Molecular Geometry tional funds are still available specifically â

Ä and Energy Calculations for Local/ for visiting fellows collaborating with ex- â

Ä perimentalists. â

HCN/HNC Ä Global Minimum and for Transition â

Ä States, Calculations of Reaction â

Ä Also discussed at the meeting are issues â

Ä Pathways, Prediction of Rate Constants related to future operations of the center, â

Ä for Organic Reactions and Isotope subscriber issues, suggestions on how to

Ä â â

Ä Effects strengthen collaboration between the â

Ä Emerson Center and BIMCORE, and how â

Ä Albert Padwa (Org. Chemistry) â

Ä to expand the scope of the center to be of â

Ä (404) 727-0283 better service to the larger community of â

Ä the University. â

Ä [email protected] â

Isomerization Wavefunction Ä Computational Studies in the Area of â Ä The committee is scheduled to meet

Contributed by Joel Bowman â

Ä Heterocyclic Chemistry and Rhodium monthly. â Ä Catalysis 3

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he Emerson Center provides powerful computational û

! ! " # " $ # % & ' ( ) Tresources and promotes active computational research in chem- û

istry, physics and related areas. The Center has an IBM9076 SP2 û û

parallel computer with 14 ThinNode-2 units (each is equivalent to û http://www.emerson.emory.edu an RS/6000 model 39H), a High Speed Switch, 4 GB of total memory û and 63 GB of disk space. The operating system of the SP2 is IBM’s û The Emerson Center web page gives the most up-to- û date information about the Emerson Center operations.

Unix version AIX accompanied by IBM’s parallel system support û product (PSSP). In addition, there are 10 IBM RS/6000 model 550 û You will have access to information about the center’s

û Mission Statement, the current list of the centers sub- workstations, one 590, and two 350s. These machines are also run- û scribers and their research interests, our Visiting Fel- ning under AIX and connected to Emory’s ethernet network, whereas û lows Program updates, software and hardware upgrade internally connected to each other via the Network File System (NFS) û

û information, news on conferences and other programs and Network Information Systems (NIS). The homogeneity of these û that the center initiates, tutorials, and links to many other AIX machines allows efficient and transparent user access by facili- û exciting sites.

tating an IBM batch queueing system product called LoadLeveler, û û

where the user submits a job to a single queue and the software dis- û patches the job to the first available CPU for execution. Parallel jobs û are executed using message passing parallel programming environ- û û Software -continued ments such as PVMe and Linda. In addition to this variety of IBM û

RISC machines the Emerson Center owns one HP workstation, model û Such software allow users to use computational methods to pre- û dict properties or assist structural analysis using molecular or

730 and one Silicon Graphics Indy 2 graphics workstation with video- û atomic scale models and rich molecular visualization capabili- output capabilities. The total computing power of these machines û ranges from 0.5 to 1 gigaflop, depending on the application used. û ties. Applications are to polymers, zeolites, catalysts, ceramics, û semiconductors, metals/alloys, organometallic, and molecular ma- û terials. They are intended to provide a convenient environment to

However, due to intensive use of our facilities the capacity limit is û carry out individual molecular mechanics calculations and semi- already sometimes reached, and therefore we plan to substantially û upgrade our hardware in the near future. û empirical, ab initio Hartree-Fock and correlated molecular orbital û calculations on diverse molecular systems. They also serve to fa- -Contributed by Dr. Stephan Irle, û cilitate processing of large numbers of closely-related calculations û as might be required to map a conformational energy profile, to System Manager, The Emerson Center û

û screen a set of compounds for a particular property or structural

û characteristic, or to parameterize a potential function for later use

û in a molecular mechanics or molecular dynamics calculation. û

û 3. MOLDEN and SciAn. Software for visualization and anima- he Emerson Center offers basic mathematical, graphical(GL), û

û tion of the research results. FORTRAN NAG and IBM’s ESSL libraries, along with dozens

T û of extremely powerful software packages, which can be divided into û 4. Data bases such as QCLDB_97. Quantum Chemical Litera- several different categories: û ture Database, for example, is an on-line application and allows û users to search quantum chemical literature. This database includes 1. Electronic structure codes, such as Gaussian-94, Gamess-96, û

û all quantum chemical papers published up to 1996.

Molpro-96.4, Cadpac-5.4, Hondo-8.4, Molcas_4.0, Turbomole/ û

TurboNMR, Mopac_93. These codes allow users to û The Emerson Center also offers Morate_4.5 and Polyrate_7.0 for

(a) optimize the geometry of the molecules, û calculations of the rate-constants of reactions. Additional soft- (b) search for transition states, û ware are added continuously upon requests from subscribers ac- (c) calculate the energy, transition dipoles, vibrational û û cording to their research needs.

frequencies, force constants, intensities for vibrations, û

polarizabilities and hyperpolarizibilities, Mulliken population û -Contributed by Dr. Jamal Musaev, analysis, multipole moments, natural population analysis, û

electrostatic potential, atomic charges, thermochemistry û Applications Software Manager, The Emerson Center û

using arbitrary isotopes, temperature and pressures. û

These packages offer semi-empirical methods (such as CNDO, INDO, û MINDO/3, MNDO, AM1, PM3, etc.), Hartree-Fock and various ver- û

sions of density functional methods, as well as the high level correla- û û tion methods such as MCSCF, MR-CISD, CCSD(T), QCISD(T), MP2, û Cherry L. Emerson Center

MP4. With these codes, users can û (a) study the potential energy surface of the complex û for Scientific Computation inorganic, organic, organometallic, biochemical reactions, at the û û Atwood Hall, 1515 Pierce Dr.

both ground and excited electronic states of the reactants, and û Atlanta, Georgia 30322 (b) search for the new materials with given physical and û Phone: (404) 727-2380 chemical properties. û û Fax: (404) 727-6586

Our message passing parallel environments such as PVM_3.2 and û

Linda that permits the use of powerful Gaussian-94, Gamess-96 and û Email: [email protected] Hondo-8.4 packages which speed up the calculations with parallel û http://www.emerson.emory.edu processing. û û This issue of the Emerson Center Newsletter 2. Molecular modeling and molecular dynamic software such as û

û is designed and edited by Jianli Zhao Cerius2, SYBYL, MM3, AMBER, Spartan_4.0, and HyperChem_4.5. 4