From s.hogg@ic.ac.uk Mon Oct 6 05:28:50 1997 Received: from romeo.ic.ac.uk for s.hogg@ic.ac.uk by www.ccl.net (8.8.3/950822.1) id FAA21073; Mon, 6 Oct 1997 05:16:32 -0400 (EDT) Received: from helen.mt.ic.ac.uk [155.198.96.140] by romeo.ic.ac.uk with smtp (Exim 1.62 #1) id 0xI9Gf-0002qQ-00; Mon, 6 Oct 1997 10:15:57 +0100 Message-Id: <3.0.3.32.19971006101100.006dd83c@155.198.100.1> X-Sender: seth@155.198.100.1 X-Mailer: QUALCOMM Windows Eudora Pro Version 3.0.3 (32) Date: Mon, 06 Oct 1997 10:11:00 +0100 To: chemistry@www.ccl.net From: Simon Hogg Subject: 2-dimensional boundary conditions Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" I have a modelling problem that is crying out for 2-d boundary conditions (solvent at surface). Unfortunately, my software only has 3-d bondary conditions. Does anyone have any coding experience of adjusting the 3-d boundary conditions so they only apply over 2 dimensions, leaving the third dimension to be modelled (semi-infinitely) -- Simon Hogg, Imperial College, London, UK Tel. +44 171 589 5111 ext. 56721 Fax. +44 171 584 3194 Email: s.hogg@ic.ac.uk Glass-List: glass-list@ic.ac.uk From widauer@inorg.chem.ethz.ch Mon Oct 6 10:28:53 1997 Received: from elwood.ethz.ch for widauer@inorg.chem.ethz.ch by www.ccl.net (8.8.3/950822.1) id KAA14190; Mon, 6 Oct 1997 10:16:44 -0400 (EDT) Received: from rosmarin (rosmarin.ethz.ch) by elwood.ethz.ch with SMTP id AA22136 (5.65c/IDA-1.4.4 for ); Mon, 6 Oct 1997 16:16:45 +0200 Message-Id: <3.0.32.19971006161423.009086a0@elwood.ethz.ch> X-Sender: widauer@elwood.ethz.ch X-Mailer: Windows Eudora Pro Version 3.0 (32) Date: Mon, 06 Oct 1997 16:14:25 +0100 To: chemistry@www.ccl.net From: Christoph Widauer Subject: all electron basis set for group V elements Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Do someone know recommended all electron basis sets for As and Sb of double or triple zeta quality including polarization functions? thanks From hao@iris.bio.ustc.edu.cn Mon Oct 6 10:51:29 1997 Received: from gateway.nic.ustc.edu.cn for hao@iris.bio.ustc.edu.cn by www.ccl.net (8.8.3/950822.1) id JAA01294; Mon, 6 Oct 1997 09:35:39 -0400 (EDT) Received: from hpe25.nic.ustc.edu.cn (hpe25.nic.ustc.edu.cn [202.38.64.1]) by gateway.nic.ustc.edu.cn (8.8.7/8.8.6) with SMTP id VAA30400 for ; Mon, 6 Oct 1997 21:17:45 +0800 Received: from iris.bio.ustc.edu.cn by hpe25.nic.ustc.edu.cn with SMTP (8.6.10/16.2) id VAA25415; Mon, 6 Oct 1997 21:11:46 +0800 Received: from localhost by iris.bio.ustc.edu.cn via SMTP (940816.SGI.8.6.9/940406.SGI) for id VAA07099; Mon, 6 Oct 1997 21:13:03 -0700 Date: Mon, 6 Oct 1997 21:13:02 -0700 (PDT) From: Hu Hao To: chemistry@www.ccl.net Subject: Re: Help for DeFT work? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=ISO-8859-1 Dear CCLers, Weeks ago I've posted a mail about the DeFT optimization of water dimer. Thanks for replies from Dr. Frederic A. Van-Catledge and Dr. Rudolf Herrmann. I have solved the problem now. There are two main reasons responsible to the results. The first is the basis sets used. The problem could be partly solved by using larger basis sets, e.g., using DZVP4 or TZVP basis as AO basis, and A3 or A4 basis as auxiliary basis. The second is as what Dr. Rudolf Herrmann said : "The functionals currently available for DF calculations are not meant to treat long range interactions such as Van der Waals forces, which should be highly important for your water dimer. DFT will be well suited for, lets say, an ice crystal, but not for this case of a water dimer." It seems that the system of water dimer needs careful consideration when studied. Sincerely Hao Hu -- _______________________________________________________________________ Hao Hu 2-615, West Campus, USTC Email: hao@iris.bio.ustc.edu.cn Hefei, Anhui 230026 WWW : (suspended) P.R.China Tel : 0551-3603754 __________________________________________________ / / / He who commands the past, controls the future; / / He who controls the future, conquers the past. / _________/ /___________ From E.Tajkhorshid@dkfz-heidelberg.de Mon Oct 6 11:28:54 1997 Received: from ns.DKFZ-Heidelberg.de for E.Tajkhorshid@dkfz-heidelberg.de by www.ccl.net (8.8.3/950822.1) id KAA19494; Mon, 6 Oct 1997 10:58:20 -0400 (EDT) Received: from cvx12.inet.dkfz-heidelberg.de (cvx12.inet.dkfz-heidelberg.de [193.174.51.101]) by ns.DKFZ-Heidelberg.de (8.7.3/DKFZ-8.6.4) with ESMTP id QAA14448; Mon, 6 Oct 1997 16:57:48 +0200 (MET DST) Received: (tajkhors@localhost) by cvx12.inet.dkfz-heidelberg.de (8.8.5/DKFZ-8.6.4) id QAA15232; Mon, 6 Oct 1997 16:57:47 +0200 (METDST) From: Emadeddin Tajkhorshid Message-Id: <199710061457.QAA15232@cvx12.inet.dkfz-heidelberg.de> Subject: volume calculation To: chemistry@www.ccl.net Date: Mon, 6 Oct 1997 16:57:47 +0200 (METDST) Cc: e.tajkhorshid@dkfz-heidelberg.de MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Dear Colleagues I am looking for programs which calculate the volume of a molecule. Any reference is highly appreciated. Thanx in advance Emad From sschulz@weasel.chemie.fu-berlin.de Mon Oct 6 14:28:53 1997 Received: from weasel.chemie.fu-berlin.de for sschulz@weasel.chemie.fu-berlin.de by www.ccl.net (8.8.3/950822.1) id OAA20636; Mon, 6 Oct 1997 14:15:07 -0400 (EDT) Received: (from sschulz@localhost) by chemie.fu-berlin.de (8.7.1/8.7.1) id UAA24002; Mon, 6 Oct 1997 20:15:11 +0200 (METDST) Date: Mon, 6 Oct 1997 20:15:10 +0200 (METDST) From: Stefan Schulz To: chemistry@www.ccl.net Subject: IR-Spectrum with GAUSSIAN 94 Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCLers, after a succesful compound optimization and frequency GAUSSIAN 94 job I get a bunch of regular output lines like this: Harmonic frequencies (cm**-1), IR intensities (KM/Mole), Raman scattering activities (A**4/AMU), Raman depolarization ratios, reduced masses (AMU), force constants (mDyne/A) and normal coordinates: 1 2 3 A' A' A" Frequencies -- 274.3467 368.7678 446.3764 Red. masses -- 6.6004 1.1200 1.1113 Frc consts -- 0.2927 0.0897 0.1305 IR Inten -- 0.2635 333.4733 1.8949 My questions are: o What does the IR-intensity unit KM/Mole mean i.e. what does KM stand for? o By which formula are the IR-intensities actually calculated? Any help will be appreciated :-) Regards Stefan Schulz =-=-=-=-this message is transmitted on 100 % recycled electrons-=-=-=-= | | | | sschulz@chemie.fu-berlin.de | Stefan Schulz | | Tel. ++49/30/838 3348 | FU Berlin - Theoretical Chemistry | | ++49/30/838 2351 | Takustrasse 3 | | FAX. ++49/30/838 4792 | D-14195 Berlin | =-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= From duanx@Picard.ml.wpafb.af.mil Mon Oct 6 15:28:55 1997 Received: from nsrhost.ml.wpafb.af.mil for duanx@Picard.ml.wpafb.af.mil by www.ccl.net (8.8.3/950822.1) id OAA20738; Mon, 6 Oct 1997 14:58:45 -0400 (EDT) Received: from Picard.ml.wpafb.af.mil by nsrhost.ml.wpafb.af.mil with SMTP (1.39.111.2/16.2) id AA273974198; Mon, 6 Oct 1997 14:56:38 -0400 Received: by Picard.ml.wpafb.af.mil (4.1/version) id AA12442; Mon, 6 Oct 97 14:58:42 EDT Date: Mon, 6 Oct 1997 14:58:42 -0400 (EDT) From: Xiaofeng Duan To: chemistry Subject: Help: TCGMSG Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII hi, all, I compiled TCGMSG (ipcv4.0) on the Origin 2000 machine to run the parallel version of GAMESS and found the maximum nodes I can use is 13. If the nodes specified is more than that, then I got system error messages. For example, if I use 14 nodes to run sample program hello.x, i got following message: hpc03-1:/hafs1/duanx/tcgmsg/ipcv4.0/ parallel hello Creating: host=hpc03-1, user=duanx, file=/hafs1/duanx/tcgmsg/ipcv4.0/hello.x, port=31271 0: SemSetCreate: n_sem has invalid value 42 (0x2a). system error message: Permission denied 14: interrupt I thought the error was caused because n_sem (Is n_sem = 3x(number of nodes)?) was larger than the default setting, therefore I redefined MAX_N_SEM in sema.c from 40 to 100. But this modification was not helpful and I got the same error. Can someone help me figure out what the problem is and how to correct it? Many thanx! **************************************** Xiaofeng Duan, Ph. D. WL/MLBP, Bldg. 654 2941 P St. Ste. 1 Wright-Patterson AFB, OH 45433 (937)255-9164 duanx@Picard.ml.wpafb.af.mil **************************************** From chem8@york.ac.uk Mon Oct 6 15:42:34 1997 Received: from lendal.york.ac.uk for chem8@york.ac.uk by www.ccl.net (8.8.3/950822.1) id PAA20764; Mon, 6 Oct 1997 15:07:52 -0400 (EDT) Received: from ebor.york.ac.uk by lendal.york.ac.uk with SMTP (PP); Mon, 6 Oct 1997 20:02:07 +0100 Received: from localhost by ebor.york.ac.uk via SMTP (950511.SGI.8.6.12.PATCH526/951211.SGI) id UAA01335; Mon, 6 Oct 1997 20:06:36 +0100 Date: Mon, 6 Oct 1997 20:06:36 +0100 (BST) From: John Waite To: Emadeddin Tajkhorshid cc: chemistry@www.ccl.net Subject: Re: CCL:volume calculation In-Reply-To: <199710061457.QAA15232@cvx12.inet.dkfz-heidelberg.de> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi Emad, Try: c volume.f - volume determination code c c Author: Lawrence R. Dodd c Doros N. Theodorou c Maintainer: Lawrence R. Dodd c Created: March 21, 1990 c Version: 2.0 c Date: 1994/07/22 15:45:51 c Keywords: volume and area determination c Time-stamp: <94/07/22 11:02:23 dodd> c Copyright (c) 1990, 1991, 1992, 1993, 1994 c by Lawrence R. Dodd and Doros N. Theodorou. C---------------------------------------------------------------------C C Plane Sphere Intersections C C---------------------------------------------------------------------C C This program will find the total and individual volume and C C exposed surface area of an arbitrary collection of spheres of C C arbitrary radii cut by an arbitrary collection of planes C C analytically by analyzing the plane/sphere intersections. C C---------------------------------------------------------------------C C Algorithm by: Doros N. Theodorou and Lawrence R. Dodd C C Coded by: L.R. Dodd C C---------------------------------------------------------------------C C Created on: March 21, 1990 C C Phase 1 Completed on: March 23, 1990 C C Phase 2 Completed on: April 16, 1990 C C Phase 3 Completed on: May 17, 1990 C C Phase 4 Completed on: June 5, 1990 C C Phase 5 Completed on: July 26, 1990 C C---------------------------------------------------------------------C C Reference: C C C C "Analytical treatment of the volume and surface area of C C molecules formed by an arbitrary collection of unequal C C spheres intersected by planes" C C C C L.R. Dodd and D.N. Theodorou C C MOLECULAR PHYSICS, Volume 72, Number 6, 1313-1345, April 1991 C C---------------------------------------------------------------------C C Acknowlegement: C C C C LRD wishes to thank his mentor DNT for a stimulating and C C enjoyable post-doctoral experience. C C---------------------------------------------------------------------C C General Notes On Program: C C C C This program has been written with an eye towards both C C efficiency and clarity. On a philosophical note, many believe C C that these ideals are mutually exclusive but in general they C C are not. There are, however, a few instances where one ideal C C has been given more prominence over the other. The comments in C C the program, together with the associated journal article, C C should help to explain any apparent logical leaps in the C C algorithm. C C C C The program was intended to be used as a subroutine called C C repeatly by some main program. In this case the subroutine C C "VOLUME" is called by some main routine which has placed the C C necessary information in common block /Raw Data/. The answers C C are returned in common block /Volume Output/. I must apologize C C for the poor input/output for the program. For example, the C C area/volume of each sphere is not placed in /Volume Output/. C C C C This program was developed on a Sun SPARCstation 330 using Sun C C FORTRAN 1.3.1 (all trademarks of Sun Microsystems, Inc.). We C C have used some of extensions to the ANSI standard including: C C C C o long variable names (i.e., more than six characters) C C o variable names containing the characters '$' and '_' C C o END DO used in place of the CONTINUE statement C C o DO-WHILE used in place of IF-GOTO constructs C C o excessive number of continuation lines in some FORMATs C C o generic intrinsic function calls (e.g., SIN for DSIN) C C o IMPLICIT NONE statement (needed in development) C C C C The advantage of using non-standard FORTRAN is that it makes it C C considerably easier to follow the flow of a program. There are C C no extraneous statement labels in this program that may have C C obscured the logic (not a single GOTO was used). The previews C C of the new F90 standard appear to adopt many of the features C C already implemented in VMS, Sun, Cray, and IBM FORTRAN. C C C C Note that this algorithm is completely parallelizable. C C C C Larry Dodd C C dodd@mycenae.cchem.berkeley.edu C C C C Department of Chemical Engineering C C College of Chemistry C C University of California at Berkeley C C Berkeley, California 94720-9989 C C (415) 643-7691 (LRD) C C (415) 643-8523 (DNT) C C (415) 642-5927 (Lab) C C C C dodd@mycenae.cchem.berkeley.edu C C doros@mycenae.cchem.berkeley.edu C C C C---------------------------------------------------------------------C C Note: C C Plane_Ordering of common block /Debug/ is, as the name C C implies, for debugging purposes only as is routine ORDERING. C C The information contain therein is not necessary for solving C C the sphere plane problem but proved incredibly useful during C C program development. C C---------------------------------------------------------------------C C Program Sphere Plane Problem Good luck, John Dr. John Waite, e-mail: chem8@york.ac.uk * or The National Hellenic Research Foundation,* john@john1.eie.gr Organic and Pharaceutical Chemistry Institute, phone: ++30-1-7238958 (direct) Vas. Konstantinou 48, phone: ++30-1-7247913(secrtry. Mary) Athens 116-35, fax: ++30-1-7247913 Greece or NCRS "Democritos", phone: ++30-1-6513112-5 X219 * c/o Dr. G.Kordas, e-mail john@john.nrcps.ariadne-t.gr Material Science Institute, Aghia Paraskevi, Attikis, Athens 153-10, Greece On Mon, 6 Oct 1997, Emadeddin Tajkhorshid wrote: > Dear Colleagues > > I am looking for programs which calculate the volume of a molecule. Any > reference is highly appreciated. > Thanx in advance > Emad > > > -------This is added Automatically by the Software-------- > -- Original Sender Envelope Address: E.Tajkhorshid@dkfz-heidelberg.de > -- Original Sender From: Address: E.Tajkhorshid@dkfz-heidelberg.de > CHEMISTRY@www.ccl.net: Everybody | CHEMISTRY-REQUEST@www.ccl.net: Coordinator > MAILSERV@www.ccl.net: HELP CHEMISTRY or HELP SEARCH | Gopher: www.ccl.net 73 > Anon. ftp: www.ccl.net | CHEMISTRY-SEARCH@www.ccl.net -- archive search > Web: http://www.ccl.net/chemistry.html > > From bruno@antas.agraria.uniss.it Mon Oct 6 17:28:55 1997 Received: from ICINECA.CINECA.IT for bruno@antas.agraria.uniss.it by www.ccl.net (8.8.3/950822.1) id QAA21157; Mon, 6 Oct 1997 16:52:22 -0400 (EDT) Received: from cinymp.cineca.it by ICINECA.CINECA.IT (IBM VM SMTP V2R2) with TCP; Mon, 06 Oct 97 22:52:53 ITA Received: from antas.agraria.uniss.it by cinymp.cineca.it with SMTP (5.61/CRI-80.1) id AA54071; Mon, 6 Oct 97 22:52:05 +0200 Date: Fri, 4 Oct 1996 19:22:21 +0100 (NFT) From: "Dr. Bruno Manunza" To: Emadeddin Tajkhorshid Cc: chemistry@www.ccl.net, e.tajkhorshid@dkfz-heidelberg.de Subject: Re: CCL:volume calculation In-Reply-To: <199710061457.QAA15232@cvx12.inet.dkfz-heidelberg.de> Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Mon, 6 Oct 1997, Emadeddin Tajkhorshid wrote: > Dear Colleagues > > I am looking for programs which calculate the volume of a molecule. Any > reference is highly appreciated. > Thanx in advance > Emad > Dear Emad, you'll find a collection of tools for calculating both volume and surface of a molecule at http://antas.agraria.uniss.it/software.html hope it helps regards 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: bruno@antas.agraria.uniss.it e-mail: bruno@tharros.dipchim.uniss.it e-mail: gx6bot81@cray.cineca.it web: http://antas.agraria.uniss.it From joerg@still3.chem.columbia.edu Mon Oct 6 17:44:05 1997 Received: from mailrelay1.cc.columbia.edu for joerg@still3.chem.columbia.edu by www.ccl.net (8.8.3/950822.1) id QAA21105; Mon, 6 Oct 1997 16:31:30 -0400 (EDT) Received: from still3.chem.columbia.edu (still3.chem.columbia.edu [128.59.112.36]) by mailrelay1.cc.columbia.edu (8.8.5/8.8.5) with SMTP id QAA18394 for <@smtp.columbia.edu:CHEMISTRY@www.ccl.net>; Mon, 6 Oct 1997 16:31:31 -0400 (EDT) Received: from still3 by still3.chem.columbia.edu via SMTP (950413.SGI.8.6.12/930416.SGI.AUTO) for id QAA17129; Mon, 6 Oct 1997 16:31:30 -0400 Sender: joerg@still3.chem.columbia.edu Message-ID: <34394AA1.41C6@still3.chem.columbia.edu> Date: Mon, 06 Oct 1997 16:31:29 -0400 From: Joerg Weiser Organization: Columbia University X-Mailer: Mozilla 3.01Gold (X11; I; IRIX64 6.2 IP25) MIME-Version: 1.0 To: CHEMISTRY@www.ccl.net Subject: Summary: Recognition of compounds from a connection table Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Some time ago, I posted the following question: "Do you know of any references that deal with the recognition of compounds (e.g stored in a compound library) from their connection tables?" I received two answers. Thanks a lot. ============================================================== Try Ash, J., Chubb, P., Ward, S., Welford, S., Willet, P., Communiaction, Storage and Retrieval of Chemical Information, Ellis Horwood Series Chemical Science, Ellis Horwood Limited, Chichester, 1985. It is not new, and some important modern developments are missing, but is is still a good overview about the basic principles and technology. Dr. Wolf-D. Ihlenfeldt Computer Chemistry Center, University of Erlangen-Nuernberg Naegelsbachstrasse 25, D-91052 Erlangen (Germany) Tel (+49)-(0)9131-85-6579 Fax (+49)-(0)9131-85-6566 ============================================================== References: Balaban, A.T.; Mekenyan, O.; Bonchev, D. : Unique Description of Chemical Structures Based on Hierarchically Ordered Extended Connectivities (HOC -Procedures). I. Algorithms for finding Graph Orbits and Canonical Numbering of Atoms., II. Mathematical Proofs, J. Comp. Chem. 1985, vol. 6, pp. 538-551. Corneil D .G., Kirkpatrick D.G. : A Theoretical Analysis of various Heuristics for the Graph Isomorphism Problem. SIAM J. Comp., 1980, v. 9, No. 2, pp. 281-297. Figueras J. : Automorphism and Equiavalence Classes. J. Chem. Inf. Comp. Sci., 1992, v. 32, pp. 153-157. Fortin S. : The Graph Isomorphism Problem. Technical Report No. TR 96-20, Dept. of Comp. Sci. University of Alberta, Edmonton, 1996. ftp://ftp.cs.ualberta.ca/pub/TechReports/1996/TR96-20/ (gzip) Golender V.E., Drboglav V.V., Rosenblit A,B. Graph Potentials Method and it's Applications for Chemical Information Processing. J. Chem.Inf.Comp.Sci., 1981, v.21, No. 4, pp. 196-204. Goodman S.E., Hedetniemi S.T., Introduction to the Design and Analysis of Algorithms McGraw-Hill, New York, 1977. Harary F. Graph Theory, Addison Wesley, Reading, MA, 1969. Hendrickson J.B., Toszko G., Unique Numbering and Cataloguing of Molecular Structures. J.Chem.Inf.Comp.Sci., 1983, v. 23, pp. 171-177. Herndon W.C. Canonical labelling and System of Linear Notation for Chemical Graphs. in Chemical Applications of Topology and Graph Theory., ed. by R.B. King, Elsevier, Amsterdam, 1983, 231-242. C. Jochum, J. Gasteiger, Canonical Numbering and Constitutional Symmetry. J. Chem.Inf.Comp.Sci., 1977, vol. 17, pp. 113-117. Liu X., Balasubramanian K., Munk M.E. : Computational Techniques for Vertex Partitioning of Graphs, J.Chem.Inf.Comp.Sci., 1990, v. 30, pp. 263-269. Liu X., Klein D. J., The graph isomorphism problem, J. Comp. Chem., 12 (1991) n. 10, 1243-1251. McKay B. D., Nauty User's Guide (version 1.5), Technical Report No. TR-CS-90-03, Comp. Sci. Dept., Australian National University, Canberra,1990. http://cs.anu.edu.au/people/bdm/nauty B. D. McKay, Practical graph isomorphism, Congressus Numerantium 30 !1981) 45-87. Miller G. L., Graph Isomorphism, General Remarks, J. Comp. Syst. Sci. 30 (1979) 128-142 Morgan H. L., The Generation of a unique machine description for chemical structures - a technique developed at Chemical Abstracts Service, J. Chem. Doc. 5 (1965), 107-113. Randic M. : On Canonical Numbering of Atoms in a Molecule and Graph Isomorphism. J.Chem.Inf.Comp.Sci., 1977, v. 17, No. 3, pp. 171-180. Razinger, M.; Balasubramanian, K.; Munk, M.E. Graph Automorphism Perception in Computer-Enhanced Structure Elucidation. J.Chem.Inf.Comp.Sci., 1993, vol. 33, pp. 197-201. Read, R.C., Corneil D.G., The Graph Isomorphism Disease, J. Graph Theory 1 (1977) 339-352. G. Rucker, C. Rucker, Computer perception of constitutional (topological) symmetry: TOPSYM, a fast algorithm for partitioning atoms and pairwise relations among atoms into equivalence classes. J.Chem. Inf. Comp. Sci., 30 (1990) 187-191. G. Rucker, C. Rucker, On Using the Adjacency Matrix Power Method for Perception of Symmetry and for Isomorphism Testing of Highly Intricate Graphs. J.Chem. Inf. Comp. Sci., 31 (1991) 123-126. Schubert W., Ugi I. : Constitutional Symmetry and Unique Description of Molecules. J. Am. Chem. Soc. 1978, v.100, No. 1, pp. 37-41. Shelley, C.A.; Munk, M.E. An Approach to the Assignment of Canonical Connection Tables and Topological Symmetry Perception. J.Chem.Ihf.Comp.Sci., 1979, vol. 19, pp. 247-250. I. V. Stankevich, E. G. Gal'pern, A. L. Chistyakov, I. I. Baskin, M. I. Skvortsova, N. S. Zefirov, O. B. Tomilin, Spectral Theory of Graphs in Chemistry. 1. Projection Operators and Canonical Numeration of Graph Vertices. J. Chem. Inf. Comp. Sci., 34 (1994) 1105-1108. Stankevitch M.I., Tratch S.S., Zefirov N.S. : Combinatorial Models and Algorithms in Chemistry. Search for Isomorphisms and Automorphisms of Molecular Graphs. J.Comp.Chem., 1988, v. 9, No. 4, pp. 303-314. M. Uchino, Algorithms for Unique and Unambiguous Coding and Symmetry Perception of Molecular Structure Diagram. I, II, III. J. Chem. Inf. Comp. Sci., 1980, 20, pp. 116-126. Ullmann, J.R. : An Algorithm for Subgraph Isomorphism. J. ACM, 1976, vol. 23, No 1, pp. 31-42. Alexander A. Oliferenko, Department of Organic Chemistry Moscow State University, Lenin Hills, Moscow 119899, Russia e-mail: alex@qsar.chem.msu.su; alex-qsar@technologist.com Phone: 7 095 939 35 57 -- ================================================================ Joerg Weiser phone: +1 212 8545143 Department of Chemistry +1 212 8548402 Columbia University 3000 Broadway MC 3140 fax: +1 212 6789039 New York, NY 10027 email: joerg@still3.chem.columbia.edu ================================================================ From adler@pulsar.cs.wku.edu Mon Oct 6 18:28:57 1997 Received: from axp1.wku.edu for adler@pulsar.cs.wku.edu by www.ccl.net (8.8.3/950822.1) id SAA21514; Mon, 6 Oct 1997 18:03:54 -0400 (EDT) Received: from pulsar.cs.wku.edu (161.6.17.52) by axp1.wku.edu (MX H5.0) with SMTP; Mon, 6 Oct 1997 17:03:55 -0500 Received: by pulsar.cs.wku.edu (SMI-8.6/SMI-SVR4) id QAA22744; Mon, 6 Oct 1997 16:58:55 -0500 From: adler@pulsar.cs.wku.edu (Allen Adler) Message-ID: <199710062158.QAA22744@pulsar.cs.wku.edu> Subject: liquids and superfluids To: chemistry@www.ccl.net Date: Mon, 6 Oct 1997 16:58:55 -0500 (CDT) CC: adler@pulsar.cs.wku.edu (Allen Adler) X-Mailer: ELM [version 2.4 PL25] MIME-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit I'm under the impression that the smallest number of molecules which can be recognized experimentally as constituting a liquid is about 70. Assuming I am not mistaken in that impression, there are two questions that occur to me: (1) can one successfully compute properties of these liquids with ab initio computations? (2) in the case of Helium, can one study the possibility and properties of the superfluid state of liquid He 4 involving such a small number of Helium atoms? If someone has already done this, I'd like to read about it. Naively, Allan Adler adler@pulsar.cs.wku.edu From uucp@msi.com Mon Oct 6 18:42:26 1997 Received: from bioc1.msi.com for uucp@msi.com by www.ccl.net (8.8.3/950822.1) id SAA21519; Mon, 6 Oct 1997 18:05:05 -0400 (EDT) Received: by bioc1.msi.com (5.64/0.0) id AA10924; Mon, 6 Oct 97 15:05:32 -0700 Received: from news.msi.com(146.202.0.224) by bioc1.msi.com via smap (V2.0) id xma010917; Mon, 6 Oct 97 15:05:14 -0700 Received: by news.msi.com (4.1/SMI-4.1) id AA08211; Mon, 6 Oct 97 14:52:46 PDT Newsgroups: msi.comp-chem-list Path: uucp From: Bob Funchess Subject: Re: CCL:2-dimensional boundary conditions X-Nntp-Posting-Host: iris76 Content-Type: text/plain; charset=us-ascii To: Simon Hogg Message-Id: <3439605A.1E01D846@msi.com> Sender: uucp@msi.com Content-Transfer-Encoding: 7bit Organization: Molecular Simulations Inc. References: <3.0.3.32.19971006101100.006dd83c@155.198.100.1> Mime-Version: 1.0 Date: Mon, 6 Oct 1997 22:04:10 GMT X-Mailer: Mozilla 4.02 [en] (X11; I; IRIX 6.2 IP22) Simon Hogg wrote: > > I have a modelling problem that is crying out for 2-d boundary > conditions (solvent at surface). > > Unfortunately, my software only has 3-d bondary conditions. Does > anyone have any coding experience of adjusting the 3-d boundary > conditions so they only apply over 2 dimensions, leaving the third > dimension to be modelled (semi-infinitely) Assuming your software allows you to set cutoff distances, the usual trick is to use 3D boundary conditions with one of the dimensions set to some very large value. If the copy in the third dimension is further away than the cutoff distance, the "layers" won't interact. -- Dr. Robert B. Funchess bobf@msi.com Senior Scientist, Scientific Support Voice (619) 458-9990 x738 Molecular Simulations Inc. FAX (619) 458-0431 9685 Scranton Road San Diego, CA 92121-3752 http://www.msi.com/