From patrick@om3.ch.umist.ac.uk Wed Oct 19 05:21:19 1994 Received: from nessie.mcc.ac.uk for patrick@om3.ch.umist.ac.uk by www.ccl.net (8.6.9/930601.1506) id EAA05248; Wed, 19 Oct 1994 04:58:42 -0400 Received: from om3.ch.umist.ac.uk (actually trigger.ch.umist.ac.uk) by nessie.mcc.ac.uk with SMTP (PP); Wed, 19 Oct 1994 09:58:16 +0100 Received: by om3.ch.umist.ac.uk (940406.SGI/) for CHEMISTRY%ccl.net@nessie.mcc.ac.uk id AA02695; Wed, 19 Oct 94 10:07:47 +0100 Date: Wed, 19 Oct 1994 10:07:46 +0100 (BST) From: patrick Subject: MO calculations on Mn complexes To: CHEMISTRY@ccl.net Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear Netters Does anybody have any references to M.O. calculations on mixed valence Mn dimers or tetramers with O or N ligands attached? Patrick J O'Malley Chemistry Dept UMIST Manchester From semper@tdc.dircon.co.uk Wed Oct 19 06:20:17 1994 Received: from felix.dircon.co.uk for semper@tdc.dircon.co.uk by www.ccl.net (8.6.9/930601.1506) id FAA05267; Wed, 19 Oct 1994 05:00:54 -0400 Received: from semper.dircon.co.uk by felix.dircon.co.uk with SMTP id AA05140 (5.67b/IDA-1.5 for ); Wed, 19 Oct 1994 09:53:52 +0100 Message-Id: <199410190853.AA05140@felix.dircon.co.uk> Sender: From: "Oliver Hill" To: CHEMISTRY@ccl.net Date: Wed, 19 Oct 1994 09:48:19 GMT Subject: Refs for BSSE in MO calcs? Reply-To: semper@dircon.co.uk Priority: normal X-Mailer: Pegasus Mail/Windows (v1.22) Dear netters Please could someone point me to some references (books or papers) that deal with Basis Set Superposition Errors (BSSE) in Ab Initio MO calculations. I have been unable to find anything in books so far. Any help will be greatly appreciated. I will summarize if there is sufficient interest/responses. Oliver PS. I have the postings from 16/17 Oct on BSSE and DFT. ______________________________________________________________________ | Oliver Hill | | | Department of Chemistry | "The true scientist never | | University of Cape Town | loses the faculty of | | Rondebosch, 7700 | amazement. It is the essence | | SOUTH AFRICA | of his(her) being." | | E-Mail:oliver@psipsy.uct.ac.za | - HANS SELYE | |--------------------------------------------------------------------| | Contact until 24 October 1994 | | | | E-Mail: semper@dircon.co.uk 1 Belgrave Place | | Tel. +44-71-235-8197 London SW1X 8BU | | Fax. +44-71-823-2112 UNITED KINGDOM | |____________________________________________________________________| From tom@dingo.niehs.nih.gov Wed Oct 19 09:21:15 1994 Received: from dingo.niehs.nih.gov for tom@dingo.niehs.nih.gov by www.ccl.net (8.6.9/930601.1506) id JAA07386; Wed, 19 Oct 1994 09:02:54 -0400 Received: by dingo.niehs.nih.gov (920330.SGI/920502.SGI.AUTO) for chemistry@ccl.net id AA15187; Wed, 19 Oct 94 05:59:56 -0700 Date: Wed, 19 Oct 94 05:59:56 -0700 From: tom@dingo.niehs.nih.gov (Thomas M. O'Connell) Message-Id: <9410191259.AA15187@dingo.niehs.nih.gov> To: chemistry@ccl.net Subject: RE: MD Constraints Dear Edgardo, Regarding your question about extending the conformational sampling of a MD run using parameter rather than algorithmic changes I would like to point out the following references. 1) Mass and Step Lenght Optimization for the Calculation of Equilibrium Properties by MD Simulations R. Pomes and J. A. McCammon, Chem. Phys. Lett 166(4) 425 1990 This paper discusses the merits of globally increasing the mass of the atoms so that a longer timestep ( several fs ) can be used, therefore facilitating longer simulations. The authors found that the rate of conformational sampling was somewhat reduced with the increased mass, but the longer dyanmics offsets this somewhat. This method is best used for calculating equilbrium thermodyamic properites, but it may be of use to you. 2) Virtual Rigid Body Dynamics T. Head-Gordon and C. L. Brooks, Biopolymers 31, 77-100, 1991 This paper is probably of more direct relevance to you. It describes a method for reduction of the full atomic representation followed by selectively constraining the system. This method is available in XPLOR 3.0 and is described in the manual. Good Luck, Tom O'C. ******************************************************* Thomas M. O'Connell Ph.D. Laboratory of Molecular Biophysics National Institute of Environmental Health Sciences tom@dingo.niehs.nih.gov ph 919-541-3872 fax -7880 From noy@tci005.uibk.ac.at Wed Oct 19 10:22:24 1994 Received: from uibk.ac.at for noy@tci005.uibk.ac.at by www.ccl.net (8.6.9/930601.1506) id JAA08395; Wed, 19 Oct 1994 09:52:58 -0400 Received: from tci005.uibk.ac.at by uibk.ac.at with SMTP id AA01467 (5.65c/IDA-1.4.4 for ); Wed, 19 Oct 1994 14:52:50 +0100 Received: by tci005.uibk.ac.at (AIX 3.2/UCB 5.64/CFIBK-2e.AIX) id AA30645; Wed, 19 Oct 1994 14:52:48 +0100 From: noy@tci005.uibk.ac.at (Noy) Message-Id: <9410191352.AA30645@tci005.uibk.ac.at> Subject: Refs for BSSE calculations To: chemistry@ccl.net Date: Wed, 19 Oct 1994 14:52:47 +0100 (NFT) In-Reply-To: <199410190853.AA05140@felix.dircon.co.uk> from "Oliver Hill" at Oct 19, 94 09:48:19 am X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 2863 : Please could someone point me to some references (books or papers) : that deal with Basis Set Superposition Errors (BSSE) in Ab Initio : MO calculations. I have been unable to find anything in books so far. : Any help will be greatly appreciated. I will summarize if there is sufficient : interest/responses. Hallo, I may give .... 1)Behera, L., Kar, T., and Sannigrahi, A.B. (1990). Effect of basis-set superposition on the atomic charges and valencies in hydrogen- and lithium-bonded complexes. Chem. Phys. Lett. 172, 487-493. This paper compares two methods for basis set superposition error corrections, namely CP (counterpoise) method invented by Boys and Bernadi and PCP (polarization counterpoise) method which takes only unoccupied orbitals as ghost orbitals. 2)Chalasinski, G., Funk, D.J., Simons, J., and Breckenridge, W.H. (1987). Moller-Plesset perturbation theory for van der Waals complexes bound by electron correlation effects: Ground states of the Ar and Mg dimers. J. Chem.Phys. 87, 3569-3579. This paper remarks how significant BSSE is in correlated level. The authors encourage the use of CP method as a resolution and well-tempered basis set to reduce BSSE. 3)Hassett, D.M., Marsden, C.J., and Smith, B.J. (1991). The ammonia dimer potential energy surface: resolution of the apparent discrepancy between theory and experiment ? Chem. Phys. Lett. 183, 449-456. This is a good example of how BSSE has created inconsistent calculation results of ammonia system. 4)Hobza, P. and Zahradnik, R. (1988). Intermolecular interactions between medium-sized systems. Nonempirical and empirical calculations of interaction energies: Success and failures. Chem. Rev. 88, 871-897. A timely review on MO calculation and its obstacles. 5)Kurdi, L., Kochanski, E., and Diercksen, G.H.F. (1985). Determination of the basis set superposition error with "DZP" basis sets in SCF calculations: CO + H2. NH3 + H2, H2 + H2. Chem. Phys. 92, 287-294. The paper shows the success of counterpoise method as the best way to go for BSSE correction. take care, Teerakiat ---------------------------------------------------------------------------- Teerakiat Kerdcharoen (NOY) Institute of General and Inorganic and Theoretical Chemistry Innrain 52a, A-6020 Innsbruck AUSTRIA e-mail: noy@tci2.uibk.ac.at, noy@tci.uibk.ac.at, c72454@cx.uibk.ac.at : noy@atc.atccu.chula.ac.th, noy@atc2.atccu.chula.ac.th ( Bangkok ) Research : Molecular Dynamics simulations : Computer Aided Molecular/Material Designs ----------------------------------------------------------------------------- *** I have no past and no future. I just have today. From A.W.J.Smith@reading.ac.uk Wed Oct 19 12:21:17 1994 Received: from mail2.rdg.ac.uk for A.W.J.Smith@reading.ac.uk by www.ccl.net (8.6.9/930601.1506) id LAA11463; Wed, 19 Oct 1994 11:50:49 -0400 Received: from scsscsc1 (actually scsscsc1.rdg.ac.uk) by suma2.rdg.ac.uk with SMTP - Local (PP); Wed, 19 Oct 1994 16:50:10 +0100 Date: Wed, 19 Oct 1994 16:50:05 +0100 (BST) From: "Andy W. J. Smith" X-Sender: scrasmit@scsscsc1 To: chemistry@ccl.net Subject: AMoO4 compounds Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Can anyone point me in the direction of any work on the tunstate or molybdate compounds. These are a series of materials including A=Co,Ni,Mn in the general formula AMoO4. There are several related structure types including wulframite,scheelite and CoMoO4 (Smith 1969). Any suitable parameters for MM, be it LJ-6-12, Buckingham (with or without shell model) would be helpful. Is anyone else working on these types of compounds? Can anyone recall any relevent papers? Currently i am tring to reproduce the crystal structures. I then want to conduct some dynamics calculations to determine high temperature cation sites and compare the results with exp. data I have collected. ANY relevent thoughts appreciated. thanks, ANDY @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ Andrew W.J. Smith Department of Chemistry, University of Reading Whiteknights, Reading, Phone: 44 (0)734-875123 ex 7441 or 4195 Berkshire, Email: A.W.J.Smith@rdg.ac.uk RG6 2AD, UK. Fax : 44 (0)734- 311610 * email is most likely to get to me first * @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@ From KGRAFTON@aardvark.ucs.uoknor.edu Wed Oct 19 13:21:22 1994 Received: from aardvark.ucs.uoknor.edu for KGRAFTON@aardvark.ucs.uoknor.edu by www.ccl.net (8.6.9/930601.1506) id MAA12456; Wed, 19 Oct 1994 12:26:44 -0400 From: Message-Id: <199410191626.MAA12456@www.ccl.net> Date: Wed, 19 Oct 94 11:28 CDT Subject: AMBER: Are Parm constraints rigid? To: CHEMISTRY@ccl.net X-VMS-To: IN%"CHEMISTRY@ccl.net" Dear CCLers, I would like to know if the constraints that may be applied to internal variables using the CONS option in Parm are indeed a rigid constraint (similar to SHAKE) or if these are actually "restraints". As a side note to this, if these are rigid constraints, why must I include the force constants in the input section? Thank you, Anthony K. Grafton Dept. of Chemistry and Biochemistry University of Oklahoma From brian@bert.chem.wsu.edu Wed Oct 19 14:22:21 1994 Received: from serval.net.wsu.edu for brian@bert.chem.wsu.edu by www.ccl.net (8.6.9/930601.1506) id NAA14526; Wed, 19 Oct 1994 13:21:24 -0400 Received: by serval.net.wsu.edu; id AA26988; Wed, 19 Oct 1994 10:21:24 -0700 Received: by bert.chem.wsu.edu (AIX 3.2/UCB 5.64/4.03) id AA16816; Wed, 19 Oct 1994 10:21:30 -0700 From: brian@bert.chem.wsu.edu (Brian W. Beck) Message-Id: <9410191721.AA16816@bert.chem.wsu.edu> Subject: Re: CCL:Amber parameters for DMF To: toba@retina.chem.psu.edu (Sam 'The Towson Tiger' Toba) Date: Wed, 19 Oct 1994 09:34:21 -0800 (PDT) Cc: DMF@bert.chem.wsu.edu, potentials@bert.chem.wsu.edu In-Reply-To: <9410190215.AA15518@retina.chem.psu.edu> from "Sam 'The Towson Tiger' Toba" at Oct 18, 94 10:15:00 pm X-Mailer: ELM [version 2.4 PL13] Mime-Version: 1.0 Content-Type: text/plain; charset=US-ASCII Content-Transfer-Encoding: 7bit Content-Length: 991 Sender: brian@bert.chem.wsu.edu Sam 'The Towson Tiger' Toba wrote: : : Dear Netters.... : : I am trying to simulate Dimethylformamide (DMF) to generate : a DMF solvent box. Structure is shown below: : Jorgensen has developed paramters for DMF. See: Author: Jorgensen-W-L and Swenson-C-J Subject: Amide Potentials Source: J.Am.Chem.Soc. 107 (1985) p569 -Brian -- ============================================================================= | .---------.| Brian W. Beck | E-mail Addresses: | |/\ | ||--------------------| INTERNET brian@bert.chem.wsu.edu | || \\ WSU || Biochem/Biophysics | BITNET F0388913@WSUVMS1 | |\ - *|| WSU , 261 Fulmer | DECNET JAGUAR::F0388913 | | | || Pullman, WA | VOICE (509) 335-4083 | | \___________|| 99164-4660 | FAX (509) 335-9688 | ============================================================================= From yuan@nka1.med.uc.edu Wed Oct 19 16:22:45 1994 Received: from nka1.med.uc.edu for yuan@nka1.med.uc.edu by www.ccl.net (8.6.9/930601.1506) id PAA19147; Wed, 19 Oct 1994 15:56:03 -0400 Received: by nka1.med.uc.edu (920330.SGI/921111.SGI.AUTO) for chemistry@ccl.net id AA08505; Wed, 19 Oct 94 15:55:43 -0400 Date: Wed, 19 Oct 1994 15:55:35 +30000 From: Jie Yuan To: Computational Chemistry List Subject: HOLE Message-Id: Mime-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi CCLers! The HOLE program can calculate pore dimensions by a Metropolis Monte Carlo mechanism (OS Smart, JM Goodfellow & BA Wallice, Biophys. J., v65, p2456, 1993). It has been run in conjunction with HYDRA or QUANTA according to Smart et al. Has HOLE been implemented in InsightII (Biosym Tech., Inc.) environment? Is it easy to do so in your opinion? Regards, Jie == Jie Yuan == Pharmacology == U. Cin. == "Jie.Yuan@UC.edu" == From vazquez@iqm.unicamp.br Wed Oct 19 19:21:22 1994 Received: from kalypso.iqm.unicamp.br for vazquez@iqm.unicamp.br by www.ccl.net (8.6.9/930601.1506) id SAA23796; Wed, 19 Oct 1994 18:49:54 -0400 Received: (vazquez@localhost) by kalypso.iqm.unicamp.br (8.6.8/8.3) id TAA00614; Wed, 19 Oct 1994 19:22:31 -0300 From: Pedro A M Vazquez Message-Id: <199410192222.TAA00614@kalypso.iqm.unicamp.br> Subject: HPCwire News Flash!!! (fwd) To: chemistry@ccl.net Date: Wed, 19 Oct 1994 19:22:30 -0300 (GMT-0300) Organization: Instituto de Quimica Unicamp X-Mailer: ELM [version 2.4 PL23] Content-Type: text Content-Length: 1510 Hello Doe anyone knows the implications of this on the future of xmol? regards Pedro Automated Mailer said: > From news@tgc.com Wed Oct 19 19:17:26 1994 > Date: Wed, 19 Oct 94 15:44:03 PDT > From: news@tgc.com (Automated Mailer) > Message-Id: <9410192244.AA19882@tgc.com> > To: vazquez@iqm.unicamp.br > Subject: HPCwire News Flash!!! > > CRAY RESEARCH COMPLETES $10.4 MILLION ACQUISITION of MSCI Oct. 19 > NEWS FLASH HPCwire > ============================================================================= > > Eagan, Minn. -- Cray Research, Inc. completed today the acquisition of > the Minnesota Supercomputer Center, Inc. (MSCI). > > Cray Research paid approximately $10.4 million cash to MSCI's owners, the > University of Minnesota and its Foundation, to acquire MSCI and its assets. > Most of the current employees at MSCI are expected to stay with Cray, the > company said, and also confirmed plans to continue the center's operation at > its current 1200 Washington Avenue South location, in Minneapolis, under the > current lease with the University. > > Following the closing, John Carlson, Cray chairman and chief executive > said, "This acquisition benefits the University, Foundation and Cray, alike. > The University and Foundation are able to realize substantial value from MSCI > while simultaneously retaining and expanding access to state-of-the-art > supercomputing systems for students and faculty members." > > From hinsenk@ERE.UMontreal.CA Wed Oct 19 20:21:23 1994 Received: from condor.CC.UMontreal.CA for hinsenk@ERE.UMontreal.CA by www.ccl.net (8.6.9/930601.1506) id TAA24505; Wed, 19 Oct 1994 19:22:43 -0400 Received: from eole.ERE.UMontreal.CA by condor.CC.UMontreal.CA with SMTP id AA10793 (5.65c/IDA-1.4.4 for CHEMISTRY@ccl.net); Wed, 19 Oct 1994 19:20:58 -0400 Received: from cyclone.ERE.UMontreal.CA by eole.ERE.UMontreal.CA (940406.SGI/5.17) id AA15193; Wed, 19 Oct 94 19:20:57 -0400 Received: by cyclone.ERE.UMontreal.CA (940406.SGI/5.17) id AA24845; Wed, 19 Oct 94 19:20:56 -0400 Date: Wed, 19 Oct 94 19:20:56 -0400 From: hinsenk@ERE.UMontreal.CA (Hinsen Konrad) Message-Id: <9410192320.AA24845@cyclone.ERE.UMontreal.CA> To: CHEMISTRY@ccl.net In-Reply-To: (message from Garcia Edgardo on Tue, 18 Oct 1994 19:45:03 -0600 (MDT)) Subject: Re: CCL:MD Constraints Edgardo Garcia writes: Is it possible to make a better sampling of conformations using MD in which the equations or algorithm are not modified but the force constants in the model are enlarged ? In this way the bonds and angles will be forced to stay almost frozen by a pronounced potential well ? That would not help. You would reduce the amplitude of the oscillations, thereby getting closer to a fixed bond length, you would at the same time increase the frequency, which is exactly what you do not want. ------------------------------------------------------------------------------- Konrad Hinsen | E-Mail: hinsenk@ere.umontreal.ca Departement de Chimie | Tel.: +1-514-343-6111 ext. 3953 Universite de Montreal | Fax: +1-514-343-7586 C.P. 6128, succ. A | Deutsch/Esperanto/English/Nederlands/ Montreal (QC) H3C 3J7 | Francais (phase experimentale) ------------------------------------------------------------------------------- From helden@gaucho.ucsb.edu Wed Oct 19 22:21:29 1994 Received: from hub.ucsb.edu for helden@gaucho.ucsb.edu by www.ccl.net (8.6.9/930601.1506) id VAA25802; Wed, 19 Oct 1994 21:36:43 -0400 Received: from gaucho.ucsb.edu by hub.ucsb.edu; id AA20241 sendmail 4.1/UCSB-2.1-sun Wed, 19 Oct 94 18:36:41 PDT for chemistry@ccl.net Received: by gaucho.ucsb.edu (AIX 3.2/UCB 5.64/4.03) id AA30875; Wed, 19 Oct 1994 18:35:07 -0700 From: helden@gaucho.ucsb.edu (Gert von Helden) Message-Id: <9410200135.AA30875@gaucho.ucsb.edu> Subject: Dielectric constant and function To: chemistry@ccl.net Date: Wed, 19 Oct 1994 18:34:56 +22305458 (PDT) Cc: helden@gaucho.ucsb.edu (Gert von Helden) X-Mailer: ELM [version 2.4 PL21] Content-Type: text Content-Length: 1215 Hi, I am rather new to the field of molecular modelling and have a question or two: I would like to model some properties of gas phase ions (macromolecules and small peptides). The charge center is usually a proton or a metal ion. The program I am using is SYBYL. The question i am having is a) out of the many option for charges, which ones are good and b) what dielectric constant and function should I use. I thought that a dielectric constant of 1 (=vacuum) that is constant is best. The other option is to use a dielectric constant that falls off with the distance. However, that seems unphysical to me and I don't see a justification for doing so. Also, looking at the force field, charge - charge induced dipole interaction (1/r^4) does not seem to be included. Are there force fields around where that interaction is included? Thanks, Gert ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + Gert von Helden, Dept. of Chemistry, UCSB, Santa Barbara, CA 93106 + + Tel : 805-893-2673, Fax : 805-893-8703 + + E-mail: helden@gaucho.ucsb.edu + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++