Computational chemistry on commodity-type computers

Journal of Chemical Information and Computer Sciences

Volumn 38, Issue 5, 1998, Pages 893-905

  Nicklaus, Marc C ^a   Williams, Robert W ^b   Bienfait, Bruno ^a   Billings, Eric S ^c   Hodošček, Milan ^c,d  

^a NATIONAL CANCER INSTITUTE   (United States)

^b UNIFORMED SERVICES UNIVERSITY OF THE HEALTH SCIENCES   (United States)

^c NATIONAL HEART LUNG AND BLOOD INSTITUTE   (United States)

^d NATIONAL INSTITUTE OF CHEMISTRY   (Slovenia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMISTRY; COMPUTER PROGRAM; INSTRUMENTATION; METHODOLOGY; MICROCOMPUTER;

CHEMISTRY; MICROCOMPUTERS; SOFTWARE;

EID: 0032161039     PISSN: 00952338     EISSN: None     Source Type: Journal    
DOI: 10.1021/ci9800920     Document Type: Article

References (19)

1. http://www.linux.org.
2. Becker, D. J.; Sterling, T.; Savarese, D.; Fryxell, B.; Olson, K. Fourth IEEE International Symposium on High Performance Distributed Computing, August 1-4, 1995, Pentagon City, VA. See, also: http:// cesdis.gsfc.nasa.gov/beowulf/.
3. Tirado-Rives, J.; Jorgensen, W. L. Viability of Molecular Modeling with Pentium-Based PCs. J. Comput. Chem. 1996, 17, 1385-1386.
4. Yu, J. S. K.; Yu, C. Benchmarks of the PC-Unix computer with electronic structure calculation. J. Chem. Inf. Comput. Sci. 1997, 37, 1111-1114.
5. http://mephisto.ca.sandia.gov/benchmarks.html; http://www.emsl.pnl. gov:2080/docs/tms/abinitio/cover.html; http://www.cc.mie-u.ac.jp/ ~ne70101/gms-bench.html; http://www.chem.joensuu.fi/people/juha _muilu/Misc/benchmarks.html.
6. http://SAL.kachinatech.eom/Z/2/; http://lem.ch.unito.it/cl/; http://www. lmcp.jussieu.fr/sincris-top/logiciel/result.html.
7. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Gill, P. M. W.; Johnson, B. G.; Robb, M. A.; Cheeseman, J. R.; Keith, T.; Petersson, G. A.; Montgomery, J. A.; Raghavachari, K.; Al-Laham, M. A.; Zakrzewski, V. G.; Ortiz, J. V.; Foresman, J. B.; Cioslowski, J.; Stefanov, B. B.; Nanayakkara, A.; Challacombe, M.; Peng, C. Y.; Ayala, P. Y.; Chen, W.; Wong, M. W.; Andres, J. L.; Replogle, E. S.; Gomperts, R.; Martin, R. L.; Fox, D. J.; Binkley, J. S.; Defrees, D. J.; Baker, J.; Stewart, J. P.; Head-Gordon, M.; Gonzalez, C.; Pople, J. A. Gaussian 94 (various revisions) is provided by Gaussian, Inc., Carnegie Office Park, Bldg. 6, Pittsburgh, PA 15106.
8. Kazushige Goto, 1-7-6, Kamimizo, Sagamihara City, Kanagawa, Japan, ZipCode 229-1123. The DGEMM library can be downloaded from ftp://ftp.eni.co.jp/.2/LinuxAlphaJP/ftp.statabo.rim.or.jp/BLAS/.
9. Durant, J. http://mephisto.ca.sandia.gov/benchmarks.html.
10. Marquez, V. E.; Ezzitouni, A.; Siddiqui, M. A.; Russ, P.; Ikeda, H.; George, C. Conformational analysis of nucleosides constructed on a bicyclo[3.1.0]hexane template. Structure-antiviral activity analysis for the northern and southern hemispheres of the pseudorotational cycle. Nucleosides Nucleotides. 1997, 16, 1431-1434.
11. Lee, C.; Yang, W.; Parr, R. G. Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density. Phys. Rev. B 1988, 37, 3098-3100.
12. Becke, A. Density-functional exchange-energy approximation with correct asymptotic behavior. Phys. Rev. A 1988, 38, 3098-3100.
13. Becke, A. Density-functional thermochemistry. III. The role of exact exchange. J. Chem. Phys. 1993, 98, 5648-5652.
14. Gaussian 92 Workshop Notes; Gaussian, Inc.: Pittsburgh, PA, 1994.
15. http://www.gnu.org/.
16. Frisch, M. J.; Frisch, Æ.; Foresman, J. B. Gaussian 94 User's Reference, Version 5.0; Gaussian, Inc.: Pittsburgh, PA, 1995;.
17. It was ascertained that none of the jobs had run "in-core" by scanning the output files for (the nonoccurrence of) the line "Two-electron integrals will be kept in memory." See Foresman, J. B.; Frisch, Æ. Exploring Chemistry with Electronic Structure Methods, 2nd ed.; Gaussian, Inc.: Pittsburgh, PA, 1996; p 31.
18. A library containing the DGEMM subroutine plus a few other functions can be downloaded from ftp://rw.usuf2.usuhs.mil/pub/libdgemm/. The file libdgemm-980415-2-coff-gnu.a can be used as a direct replacement for the DXML library in the make file command "ESSLIB = -ldxml".
19. This subroutine has been placed under the GNU Library Public License. For its text, see, e.g.: http://www.netppl.fi/~pp/glibc/libc_32. html.