From lim@rani.chem.yale.edu Wed Sep 30 20:53:50 1992 From: Dongchul Lim Subject: Re: perl scripts for modes extraction To: chemistry@ccl.net (Computational Chemistry) Date: Thu, 1 Oct 92 0:53:50 EDT jkl@ccl.net writes: > > Dear Netters, > > There is also a readme file in /pub/chemistry/perl/vibmodes which tells you > how to use these programs. If you are using OSCPOST e-mail interface, > request files: ./perl/vibmodes/DGAUSSmodes.perl, ./perl/vibmodes/DMOLmodes.perl > ./perl/vibmodes/G90modes.perl, ./perl/vibmodes/readme by sending message: > [... a lot of stuff deleted ...] > #!/usr/local/bin/perl > > # Script to extract nomrmal modes from the G90 output file. > # The OUT file may be the result of single calculations with > # link line (like example 6.15 in G90 manual) or a result of > # a separate restart with FREQ keyword from checkpoint file. > # The first task is to find out if OUT contains two runs > # (geometry optimization followed by frequences) or just one. > # Then if 2 runs, skip the portion of file up to and including > # first @ (it ends the result summary portion for geometry optimization). > # Then search for "Z-Matrix orientation:" string, skip > # 4 lines and collect cartesian coordinates in the array > # until you reach line of "--------------". Count the atoms. > # Then search for the "Frequencies ---" string, which > # starts first portion of the table of frequences and > # normal modes. It looks like: [... a lot of stuff deleted ...] > Jan Labanowski > Ohio Supercomputer Center > jkl@ccl.net The above comments were taken from 'G90modes.perl' which can be found in 'perl' directory on www.ccl.net. I didn't try this perl script (we haven't installed perl on our system yet.), but it seems that the script extracts the cartesian coordinates in zmatrix orientation rather than standard orientation. Quoting from Gaussian 90 manual (page 172), When evaluation of the second derivatives is complete, link 716 analyzes the vibrational modes. Its output includes: * the dipole moment and the polarizability and hyperpolarizability tensors, in the STANDARD ORIENTATION and atomic units. * the vibrational frequencies and the associated normal modes. these are also in the STANDARD rather than Z-matrix orientation. ^^^^^^^^ (beat me if I'm wrong) Remedy is simple. Just replace the line containing last if /Z-Matrix orientation:/ with last if /Standard orientation:/ Then this perl script will be a very useful chemistry tool, for extracting coordinates, frequencies, normal modes etc. for further application. -DCL Department of Chemistry Yale University From nauss@wrair-emh1.army.mil Mon Oct 1 04:36:00 1992 Date: 1 Oct 92 09:36:00 EST From: nauss@wrair-emh1.army.mil Subject: Starting conformations for MD runs To: "chemistry" Good day - I am conducting conformational searches of peptides using molecular dynamics and energy minimization techniques. I am concerned about what starting conformation(s) to use for my peptides. Currently, I am using an extended chain conformation with several hundred steps of steepest descents minimization to obtain an initial conformation. However, I seem to recall that there is a published list of low energy conformations for all dipeptide combinations. These sets of phi-psi angles would perhaps allow a different set of initial conformations to study. Does anyone recall such a reference? I vaguely recall the work was by Scheraga and coworkers. Thanks for your interest... Jeffrey Nauss -------------------------------------------------------------------------------- E-mail address: nauss@wrair-emh1.army.mil Mailing Address: Department of Gastroenterology Division of Medicine Walter Reed Army Institute of Research ATTN: MAJ Jeffrey L. Nauss, Ph.D. Washington, D.C. 20307-5100 Telephone: 202-576-3485 From kmoore@ncsc.org Thu Oct 1 06:26:54 1992 Date: Thu, 1 Oct 92 10:26:54 EDT From: Kevin Moore To: smb@smb.chem.niu.edu Subject: International AVS Center Steve, The AVS center is heavily involved in porting AVS modules to each of the platforms represented by the members of the AVS consortium. Most of these modules are available via anonymous ftp from avs.ncsc.org (128.109.178.23). They also are involved with answering questions about avs. Send your questions about avs or about the AVS center in general to avs@ncsc.org. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ || Kevin Moore North Carolina Supercomputing Center || || Scientific Support Analyst 3021 Cornwallis Rd. || || (919) 248-1179 Research Triangle Park, NC 27709 || ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From jkl@ccl.net Thu Oct 1 06:21:47 1992 Date: Thu, 1 Oct 1992 10:21:47 -0400 From: jkl@ccl.net To: lim@rani.chem.yale.edu Subject: Re: perl scripts for modes extraction Dongchul, Thank you for your comments on perl modes extraction from G90. I wanted to note here that "Standard orientation" appears in the G90 output file only if you use symmetry. If you do not use symmetry, the "Standard orientation" never appears in the output file and Z-matrix orientation is "Standard orientation". I will modify the scripts to check if symmetry is used, and if so, the search will be after "Standard orientation" rather than "Z-matrix orientation". The script simply reflects my preference not to use symmetry even if it is there (apparently). Jan Ohio Supercomputer Center jkl@ccl.net From B314U05@UTARLG.UTA.EDU Thu Oct 1 05:38:00 1992 Date: Thu, 1 Oct 1992 10:38 CDT From: B314U05@UTARLG.UTA.EDU Subject: Cambridge Structural Database To: chemistry@ccl.net Dear Netters, We have the Biosym software. Can we interface the Cambridge Structural Database (CSD) with Biosym? If so, can someone please tell me where to send our requests for CSD and the cost of it? Thanks in advance pavan e.mail: b314u05@utarlg.uta.edu From UCTN004@FRORS31.bitnet Mon Oct 1 03:58:23 1992 Date: 01 Oct 92 07:58:23 EDT From: "M. Fares" Subject: ALCHEMY To: chemistry@ccl.net good morning, I use the ALCHEMY II program from MOTECC, it is a ab initio package using Slater type orbitals for linear molecules. I would contact evryone who use it and discuss on it and more on the integral part because there is nofull d M. Fares e-mail : Uctn004 at frors31.bitnet Thanks M. Fares From J_BROWN@uvmvax.uvm.edu Thu Oct 1 08:52:00 1992 Date: Thu, 1 Oct 1992 13:52 EST From: J_BROWN@uvmvax.uvm.edu Subject: REQUEST HELP FINDING pKa AND BOND STRENGTHS OF O-XYLENE To: CHEMISTRY@ccl.net Could someone please tell me where I could find pKa values and bond strenghts (experimental and/or theoretical) for the aromatic and methyl C-H bonds of o-xylene (Benzene 1,2 dimethyl [95-47-6]) Thank you, Jay Brown J_BROWN@UVMVAX.BITNET From rsjuds@snll-arpagw.llnl.gov Thu Oct 1 06:04:02 1992 Date: Thu, 1 Oct 92 13:04:02 -0700 From: rsjuds@snll-arpagw.llnl.gov (judson richard s) To: chemistry@ccl.net Subject: Spherical vs. Periodic Boundary Conditions Dear Netters, Can anyone give me some information on the relative merits of using periodic boundary conditions vs. spherical boundary conditions (imposed with a soft wall at a specified radius) for doing large water simulations? How is accuracy affected? Does one option give answers of a specified quality with fewer ware molecules than the other? What sort of properties are not accurately calculable with one option or the other. Any information or references are appreciated. ----------------------------------------------- | Richard Judson | | Center for Computational Engineering | | Sandia National Laboratories | | Livermore, CA 94551-0969 | | (510)294-1438 | | email: rsjuds@sandia.llnl.gov | | | ----------------------------------------------- From rjb@qm.c-chem.siu.edu Thu Oct 1 06:30:19 1992 Organization: Southern Illinois University at Carbondale To: chemistry@ccl.net (CompChem Discussion) From: rjb@qm.c-chem.siu.edu (Robert Brenstein) Date: Thu, 1 Oct 1992 12:30:19 CST Subject: Re: > Public Domain Chemistr Reply RE>> Public Domain Chemistry > I have been asked by a friend if their are any public >domain chemistry packages for the Macintosh that would be appropriate >for use in high school chemistry classes. Not being totally familiar >with what is available, I thought I'd ask the net. You can respond to >the net or to me personally. Thanks for your help. Check out MacSciTech's anonymous ftp (ra.nrl.navy.mil 128.60.0.21). They have chemistry-related directory with a collection of various things. Robert From pollanen@csc.fi Fri Oct 2 01:44:54 1992 From: Raimo Pollanen Subject: Is there any program(s) available to translate a file from Discover (cartesian) coordinates to X-ray diffraction form of coordinates To: chemistry@ccl.net Date: Thu, 1 Oct 1992 23:44:54 +0200 (EET) Hello Can you help me in this kind of problem: I have done energy minimizations with Discover programs and now I want to compare this file (file.car or .cor) to those in X-ray diffraction database coordinate files Is it possible? And if it is - How? I want to compare two files and another has to be changed from cartesian coordinate form to X-ray form ...? Yours Raimo Pollanen Pollanen@convex.csc.fi From R1JJH@VM1.CC.UAKRON.EDU Thu Oct 1 13:30:26 1992 Date: Thu, 01 Oct 92 17:30:26 EDT From: Jack Houser Subject: PC problem alert To: Supercomputer bulletin board Dear Netters: A colleague discovered the following problem and suggested that I pass it on to the computational community, given the popularity of PCs. Jack Houser Department of Chemistry The University of Akron Akron, OH 44325-3601 Subject: Numerical instabilities on PC's We have found mumerical instabilities for matrix diagonalizations on certain PC's. The same Microsoft Fortran 5.1 double precision executable module was used on all PC's; Sun Fortran was used under UNIX on the SPARC station. Using a 111x111 relatively sparse matrix and a Jacobi rotation routine, a Compuadd 286 PC produced inaccurate eigenvalues. However, a Gateway 386 PC, a SPARC station IPC (UNIX) and the SPARC station running Microsoft Fortran under Soft-PC all produced correct results. For this test the Gateway 386 was stable up to the maximum size tested, 150x150. The SPARC station has shown no instability up to 550x550. Under previous tests, 3 different Compuadd 286 PC's all produced identical erroneous results. These 286 PC's all produced accurate results for relatively small matrices. But the inaccuracies began at some threshold matrix dimension (typically 40 to 100) and rapidly increased in magnitude until the results were unrecognizable. Symptoms include failure to reproduce rigorous degeneracies and unnormalized eigenvectors. The precise threshold depends on the nature of the matrix and on the particular diagonalization algorithm. The faster Householder method is less stable than Jacobi rotations. From these tests we conclude that MS Fortran itself is OK. The problem might David Perry From pfu@ritz.math.fu-berlin.de Thu Oct 1 22:50:21 1992 Date: Thu, 1 Oct 92 16:44 MET From: pfu@math.fu-berlin.de (Ping Fu) To: chemistry@ccl.net Subject: Protein Phrenology National Center for Supercomputing Applications (NCSA) has recently released a new geometric software with 3D graphic user interface, the tool is called Alvis (Alpha Shape Visualizer). One can use Alvis to construct and compute 3D structures of molecules (proteins). The input to Alvis is any scattered point set (x, y, z coordinates in 3D sapce), and one can render it's disired shape, or output it's solid or surface mesh. A short description of 3D alpha shapes -------------------------------------- Frequently, data in scientific computing is in its abstract form a finite point set in space, and it is sometimes useful or required to compute what one might call the "shape" of the set. For that purpose, we introduced the formal notion of the family of alpha shapes of a finite point set in 3D space, R^3. Each shape is a polytope, derived from the Delaunay triangulation of the point set, with a parameter alpha controlling the desired level of detail. The employed algorithms construct the entire family of shapes for a given set of size n in worst-case time O(n^2). Conceptually, alpha shapes are a generalization of the convex hull of a point set. Let S be a finite set in R^3 and alpha a non-negative real number. The alpha shape of S is a polytope that is neither necessarily convex nor connected. For alpha = infinity, the alpha shape is identical to the convex hull of S. However, as alpha decreases, the shape shrinks by gradually developing cavities. These cavities may join to form tunnels, and even closed holes can be computed. Intuitively, a piece of the polytope disappears when alpha becomes small enough so that a sphere with radius alpha, or several such spheres, can occupy its space without enclosing any of the points of S. Think of R^3 filled with Styrofoam and the points of S made of more solid material, such as rock. Now imagine a spherical eraser with radius alpha. It is omnipresent in the sense that it carves out Styrofoam at all positions where it does not enclose any of the sprinkled rocks, that is, points of S. The resulting object is called the alpha hull. To make things more feasible, we straighten the object's surface by substituting straight edges for the circular ones and triangles for the spherical caps. The thus obtained object is the alpha shape of S. It is a polytope in a fairly general sense: it can be concave and even disconnected, it can contain two-dimensional patches of triangles and one-dimensional strings of edges, and its components can be as small as single points. The parameter alpha controls the maximum ``curvature'' of any cavity of the polytope. A paper is distributed with the software for people who are interested in the formal definitons. The software is available via NCSA anonymous ftp server. ftp ftp.ncsa.uiuc.edu or ftp 141.142.20.50 Login: anonymous passwd: your login once you are in the main directory please do cd SGI/Alpha-shapes In this directory, one can find the software and the paper. Currently the graphic user interface only runs on SGI workstations. NOTE NOTE NOTE -------------- Please do not send your email directly to me since I am currently in Germany. Sending your email to alpha@ncsa.uiuc.edu will give you much better response. Ping Fu Software Development Group NCSA, University of Illinois Urbana-Champaign From C1790@slvaxa.umsl.edu Thu Oct 1 11:07:00 1992 Date: Thu, 1 Oct 1992 17:07 CST From: C1790@slvaxa.umsl.edu Subject: PHONE NUMBER FOR THE BROOKHAVEN PROTEIN DATA BANK To: CHEMISTRY@ccl.net DEAR NETTERS, WOULD SOMEONE GIVE ME THE PHONE NUMBER FOR ORDERING THE PDB STRUCTURAL DATABASE. THANKS, BILL WELSH (C1790@UMSLVAXA) From DSOUTH@uoft02.utoledo.edu Mon Oct 1 17:37:45 1992 Date: 01 Oct 1992 21:37:45 -0400 (EDT) From: DSOUTH@uoft02.utoledo.edu Subject: Re: PC problem alert To: chemistry@ccl.net From: IN%"R1JJH@VM1.CC.UAKRON.EDU" "Jack Houser" 1-OCT-1992 21:12:57.25 To: IN%"chemistry@ccl.net" "Supercomputer bulletin board" CC: Subj: PC problem alert Return-path: Received: from oscsunb.ccl.net by UOFT02.UTOLEDO.EDU (PMDF #2338 ) id <01GPG5MXH0WW002WEB@UOFT02.UTOLEDO.EDU>; Thu, 1 Oct 1992 21:12:29 EDT Received: by oscsunb.ccl.net (5.65c+KVa/920330.1102) id AA25455; Thu, 1 Oct 1992 17:56:07 -0400 Received: from VM1.CC.UAKRON.EDU for jkl by oscsunb.ccl.net (5.65c+KVa/920330.1102) id AA25145; Thu, 1 Oct 1992 21:38:23 GMT Received: from VM1.CC.UAKRON.EDU by VM1.CC.UAKRON.EDU (IBM VM SMTP V2R1) with BSMTP id 1389; Thu, 01 Oct 92 17:36:50 EDT Received: from AKRONVM (R1JJH) by VM1.CC.UAKRON.EDU (Mailer R2.08 R208004) with BSMTP id 3154; Thu, 01 Oct 92 17:34:55 EDT Date: 01 Oct 1992 17:30:26 -0400 (EDT) From: Jack Houser Subject: PC problem alert Sender: chemistry-request@ccl.net To: Supercomputer bulletin board Errors-to: owner-chemistry@ccl.net Message-id: <199210012138.AA25145@oscsunb.ccl.net> X-Envelope-to: CULMER, dsmith, DSOUTH, fax0314, fax0540, GRX0633, grx1010, JADAMS, JBITAR, JGano, LFINDSE Content-transfer-encoding: 7BIT Precedence: bulk Dear Netters: A colleague discovered the following problem and suggested that I pass it on to the computational community, given the popularity of PCs. Jack Houser Department of Chemistry The University of Akron Akron, OH 44325-3601 Subject: Numerical instabilities on PC's We have found mumerical instabilities for matrix diagonalizations on certain PC's. The same Microsoft Fortran 5.1 double precision executable module was used on all PC's; Sun Fortran was used under UNIX on the SPARC station. Using a 111x111 relatively sparse matrix and a Jacobi rotation routine, a Compuadd 286 PC produced inaccurate eigenvalues. However, a Gateway 386 PC, a SPARC station IPC (UNIX) and the SPARC station running Microsoft Fortran under Soft-PC all produced correct results. For this test the Gateway 386 was stable up to the maximum size tested, 150x150. The SPARC station has shown no instability up to 550x550. Under previous tests, 3 different Compuadd 286 PC's all produced identical erroneous results. These 286 PC's all produced accurate results for relatively small matrices. But the inaccuracies began at some threshold matrix dimension (typically 40 to 100) and rapidly increased in magnitude until the results were unrecognizable. Symptoms include failure to reproduce rigorous degeneracies and unnormalized eigenvectors. The precise threshold depends on the nature of the matrix and on the particular diagonalization algorithm. The faster Householder method is less stable than Jacobi rotations. From these tests we conclude that MS Fortran itself is OK. The problem might David Perry --- Administrivia: This message is automatically appended by the mail exploder: CHEMISTRY@ccl.net: --- everyone CHEMISTRY-REQUEST@ccl.net: --- coordinator OSCPOST@ccl.net: send help from chemistry Anon. ftp: www.ccl.net --- From DSOUTH@uoft02.utoledo.edu Mon Oct 1 18:53:01 1992 Date: 01 Oct 1992 22:53:01 -0400 (EDT) From: DSOUTH@uoft02.utoledo.edu Subject: Re: PC problem alert To: chemistry@ccl.net /* My sincerest apologies for the copy of this message */ /* that "escaped" prematurely. No bandwith waste */ /* intended. (gee, I guess MAIL /EDIT _isn't_ fully */ /* global under VMS.) */ >Subject: Numerical instabilities on PC's >We have found mumerical instabilities for matrix diagonalizations on certain >PC's. The same Microsoft Fortran 5.1 double precision executable module was >used on all PC's; Sun Fortran was used under UNIX on the SPARC station. >Using a 111x111 relatively sparse matrix and a Jacobi rotation routine, >a Compuadd 286 PC produced inaccurate eigenvalues. However, a Gateway 386 PC, >a SPARC station IPC (UNIX) and the SPARC station running Microsoft Fortran >under Soft-PC all produced correct results. For this test the Gateway 386 was >stable up to the maximum size tested, 150x150. The SPARC station has shown no >instability up to 550x550. I assume that the gestalts of the various PC's varied only in manufacture. (a.k.a. They were all running the same DOS revision, TSR's, network/mouse/?? drivers). Though other that the differences in BIOS, none of these would be a likely canidate for the type of numerical inaccuracies described. >Under previous tests, 3 different Compuadd 286 PC's all produced >identical erroneous results. These 286 PC's all produced accurate >results for relatively small matrices. But the inaccuracies began >at some threshold matrix dimension (typically 40 to 100) and rapidly >increased in magnitude until the results were unrecognizable. Symptoms >include failure to reproduce rigorous degeneracies and unnormalized >eigenvectors. The precise threshold depends on the nature of the >matrix and on the particular diagonalization algorithm. The faster >Householder method is less stable than Jacobi rotations. Out of interest, were the matricies permuted with smaller elements to the upper-left-hand corner? If memory serves the "standard" implementation of the Householder reduction is preformed from the bottom-right corner -- large variations in element magnitude there will cause considerable rounding errors. >From these tests we conclude that MS Fortran itself is OK. The >problem might be specific to certain Compuadd machines but I >have heard related complaints about rounding errors from >colleagues so I suspect that it may be general to the Intel 286 chip. Well, if it is producing binaries that give large variations in results across supposedly "compatable" platforms, I might be a bit suspect about their math libraries "hardware dependance" (perhaps a check for the IEEE aproved accuracy??). But then again, I am a bit suspect of everyone's math libraries after reading Plauger's book. -- /* Dale Southard Jr. -- Smith Research Group Sr. Rigger */ /* Department of Chemistry AFF/I SL/I */ /* University of Toledo D-11216 */ /* dsouth@uoft02.utoledo.edu -- "Just another skydiving grad student." */