From jkl@ccl.net Fri Mar 15 13:57:45 1991 Date: Fri, 15 Mar 91 13:39:37 EST From: jkl@ccl.net Subject: Computational CHemistry List is back To: chemistry@ccl.net Status: R The Computational Chemistry List is BACK. I will start distributing messages which accumulated since the list was stopped. Please, be patient. They will all be coming with FROM: line from me, but the original contributors will be also shown. Jan Labanowski jkl@ccl.net JKL@OHSTPY.BITNET --- From chemistry-request@ccl.net Fri Mar 15 14:27:25 1991 Date: Fri, 15 Mar 91 19:11:26 GMT From: "James P. Schmidt" Subject: I am curious to know whether anyone has worked with MOPAC 5.0 To: chemistry@ccl.net Status: R Please excuse the erroneous subject line. I am curious to know whether anyone has worked with MOPAC 5.0 on an IBM PC. If so what compiler did you use to get it running, were you able to find a way around the 640-kb memory barrier, and of course was it in fact worth the attempt given the limitations of the machine. Jim Schmidt University of Rochester jims@duce.medicine.rochester.edu --- From jkl@ccl.net Fri Mar 15 15:25:51 1991 Date: Fri, 15 Mar 91 15:10:10 EST From: jkl@ccl.net Subject: More bugs in basis set intro To: chemistry@ccl.net Status: R Mike Zerner (zerner@qtp.ufl.edu Thu Mar 7 19:06:08 1991) found more bad stuff in my basis set intro. I am really glad that the person of his experience took the time to read it and write the comments to correct me. Here are his comments and my "answers": Jan Labanowski jkl@ccl.net -------------------------------------------------------------------------- MZ> One of the reasons that core orbitals make their appearance in valence MZ> and other higher energy orbitals is due to the fact that all mo's must be MZ> orthogonal. If one examines these coefficients they are very much like MZ> those you would get from simple Schmidt orthogonalisation to the lower MZ> lying core orbitals. JL> Hi Mike, JL> JL> I aggree with you that some of my statements in the "Basis Sets Trilogy" JL> are at least misleading, if not plain wrong. Only after I heard people's JL> comments I realised that what I wanted to say and what I actually said are JL> two different things. Of course, there are two major reasons for this: JL> 1) I am truly ignorant is many of these issues, 2) I wanted to be brief, JL> JL> My statement that core orbitals are present in HOMO. JL> What I wanted to imply was: if the basis functions were "true" atomic JL> orbitals (i.e. all atomic orbitals on a given center were orthogonal to JL> each other and overlap between "core" orbitals on different centers was JL> negligible) we would not have large participation of core orbitals in HOMO. JL> But it seems that I am totally wrong on this. Please help me,since I simply JL> do not know. Of course, I probably should go and retake a course "Quantum JL> Chemistry for Psychologists 100" but I do not have time. This perception JL> comes from my early years when they showed me this diagram for homonuclear JL> molecule. If what I said above is not true than these molecular JL> orbital diagrams are totally misleading and should be abolished. JL> I would really appreciate your comment on this. ---------------------------------------------------------------------------- MZ> I don't understand the discusion above the 66-31 basis set for Si Table. MZ> If a primitive occurs contracted in a 3 combo , say, x+y+z, and appears MZ> by itself, say z, why is this linearly dependent? I.e think of three MZ> dimensional space. DId I read this wrong? JL> Linear independence. Yes, I did say something else than I wanted to say. JL> Basis functions: JL> phi_1 = a_1*g_1 + a_2*g_2 + a_3*g_3 (set I) JL> phi_2 = g_3 JL> are not linearly dependent. JL> What I wanted to say is that basis functions JL> phi_1' = a_1'*g_1 + a_2'*g_2 (set II) JL> phi_2 = g_3 JL> would yield the basis set of exactly the same quality with the following JL> relationship between coefficients in resulting molecular orbitals: JL> JL> ... c_1*phi_1 + c_2*phi_2 ... (set I) JL> and JL> ... c_1*phi_1' + (c_1*a_3 + c_2)*g_3 (Set II) JL> JL> However, since set with "doubled" g_3 (set I) whould take more time at JL> integral calculation stage (assuming no support for general JL> contractions), it would be wasteful not to use basis set II. ---------------------------------------------------------------------------- MZ> under 66-31G means that there is :" should this not be S(6/6/3/1) rather MZ> than S(6/6/3/2) ? JL> 66-31G -> is s(6/6/3/1) and not s(6/6/3/2) and it is a typo (another one). ---------------------------------------------------------------------------- MS> The difference between the 2p function on Li, and the 3d on S, is that the MS> former is needed for hybridization, and ignoring it ignores all of first MS> year chemistry! (The first solid state calculations on Li and alkali MS> halides were done by physists, and of course, did not contain the 2p!). MS> The 3d function on sulfur is usually polarization, but even this is MS> somewhat controversial. JL> p's for Li and d's for S. What I wanted to say is, that designating JL> a function as "polarization" or "basic" should not be based on how JL> obvious or not obvious it is. I would welcome some more precise criterion, JL> since "accuracy of the results" and "correctness of physical picture" is JL> very subjective (depends on the investigator) and depends on the particular JL> system studied. ---------------------------------------------------------------------------- --- From chemistry-request@ccl.net Fri Mar 15 21:25:10 1991 Date: Fri, 15 Mar 1991 18:08:03 PST From: "W. Todd Wipke" Subject: wanted: Alpha testers for MAGIC To: chemistry@ccl.net Status: R From: SECS::WIPKE "W. Todd Wipke" 15-MAR-1991 18:04:41.58 To: MX%"sci-chem@usenet",MX%"bionet-software@usenet" CC: MX%"chemistry@osu.edu",WIPKE Subj: wanted: Alpha testers for MAGIC We are looking for people interested in alpha testing a system for communication and viewing of molecular dynamics trajectories. To qualify you should have dynamics trajectories that you have generated, and have available a PC, Mac, Sun, or Vaxstation, or Amiga. If you are interested in providing feedback on the MAGIC system, send e-mail to wipke@secs.ucsc.edu including what computer equipment you would use for viewing and what the name of the dynamics program you use is. If you have any famous trajectories that have been the subject of a publication, we would be interested in obtaining them as demonstration trajectories. The source of the trajectories will be displayed as credit for the contribution. Part of MAGIC is HOCUS, which converts the dynamics history file into a machine-independent format. We have a HOCUS for DISCOVER/INSIGHT, but need volunteers to do the HOCUS for the major dynamics programs that are available. If you have your own home-grown dynamics program, you will be interested in developing a HOCUS for it for your own use and we will be interested to know if our format instructions are clear and adequate for you to accomplish that. A description of other parts of the system, POCUS, SMOKE, and MIRRORS will be available to those alpha testers selected. Anyone who has an IBM 6000 or HP workstation that would like to be involved in a port to that box is welcome to apply. Our goal is to have ports for every major platform and every major dynamics program. Language=C reply to wipke@secs.ucsc.edu 25th anniversary "Where innovation is a tradition" ---