From chemistry-request@server.ccl.net Mon Jan 8 00:17:45 2001 Received: from chem.ufl.edu (server.chem.ufl.edu [128.227.16.141]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f085Hjp02406 for ; Mon, 8 Jan 2001 00:17:45 -0500 Received: from chem.ufl.edu (chem.ufl.edu [128.227.16.141]) by chem.ufl.edu (8.9.1/8.9.1/map) with ESMTP id AAA26679 for ; Mon, 8 Jan 2001 00:16:25 -0500 (EST) Date: Mon, 8 Jan 2001 00:16:25 -0500 (EST) From: "Xiang(Simon) Wang" To: CHEMISTRY@ccl.net Subject: MOLVIB Module in Charmm Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Dear CCLers: Can someone give me more details about how to use MOLVIB Module in Charmm? More specifically, about the analysis of GAUSSIAN output( Keyword: GAUS ). There is no testcases available for MOLVIB. Any assistance would be highly appreciated. Thanks, Simon WANG From chemistry-request@server.ccl.net Mon Jan 8 04:32:33 2001 Received: from info.cyf-kr.edu.pl (info.cyf-kr.edu.pl [149.156.4.11]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f089WVp02738 for ; Mon, 8 Jan 2001 04:32:31 -0500 Received: from kinga.cyf-kr.edu.pl (kinga.cyf-kr.edu.pl [149.156.2.32]) by info.cyf-kr.edu.pl (8.9.3/8.9.3) with ESMTP id KAA19972 for ; Mon, 8 Jan 2001 10:29:05 +0100 (MET) Received: (from mykrol@localhost) by kinga.cyf-kr.edu.pl (8.9.3/8.9.3) id KAA28992; Mon, 8 Jan 2001 10:28:31 +0100 (MET) Date: Mon, 8 Jan 2001 10:28:27 +0100 (MET) From: Marcin Krol To: Subject: CHARMM --> GROMOS trajectory In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Dear CCL'ers I'm looking for a program to convert CHARMM binary trajectory to GROMOS trajectory file. Thanks in advance for your help Marcin Krol From chemistry-request@server.ccl.net Mon Jan 8 05:32:37 2001 Received: from sirene.rz.uni-duesseldorf.de (sirene.rz.uni-duesseldorf.de [134.99.128.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08AWbp02858 for ; Mon, 8 Jan 2001 05:32:37 -0500 Received: from koronium (koronium.ac2.uni-duesseldorf.de [134.99.76.30]) by neptun.rz.uni-duesseldorf.de (Sun Internet Mail Server sims.4.0.2000.05.17.04.13.p6) with SMTP id <0G6U00EA8AK21P@neptun.rz.uni-duesseldorf.de> for CHEMISTRY@ccl.net; Mon, 8 Jan 2001 11:31:14 +0100 (MET) Date: Mon, 08 Jan 2001 11:42:27 +0100 From: Stefan Konietzny Subject: Question about =?iso-8859-1?q?ECP=B4s=20and=20Basis=20Sets?= In-reply-to: To: CHEMISTRY@ccl.net Message-id: <01010514402700.01598@koronium> Organization: Institut =?iso-8859-1?q?f=FCr=20Anorganische=20Chemie=20und=20Strukturchemie?= MIME-version: 1.0 X-Mailer: KMail [version 1.1.99] Content-type: text/plain; charset=US-ASCII Content-transfer-encoding: 7BIT References: I am not sure if this message got thru over the weekend, i sent it again, because confusion is getting worse. Dear CCLers, i have two questions about the usage of ECPs. In Gaussian98 the ECPs and the related basis sets by Stevens,Basch,Kraus are implemented and are called by the keyword CEP4G. When i type CEP4G* i get a polarization function with (for Bi) d-exponent of zero. This makes no sense for me and is, if one uses not gfprint or gfinput to check the basis, very dangerous. By the way, it is not a minimal basis with four primitives but a valence double zeta with (41/41) contraction. In a table in the manual (p36) it is noted that polarization functions are not available for SDD ECP/Basissets but i get a d-function when i call SDD for Bismuth. I woukd like to optimize d-functions on my own. Q1: Is it accurate to optimize d-polarization functions on atoms by varying the exponent and minimizing the energy on a level that takes electron correlation into account (say CISD), like Frenking (chem. phys. lett. 1993, 208, p237) did for the Hay and Wadt ECPs? Or should one calculate a few model compounds, like hydrides, halogenides or methyl substituted molecules and find a mean value for the exponent by minimizing the energy of those compounds? Q2: When i use an ECP for a heavy element like Bismuth, must i use an ECP and the corresponding basis of the same "family" for the lighter elements as well, or is it OK to use an all electron basis set with the same quality of the valence shell: For example to use 6-31g* together with SDD (Stuttgart, Dresden ECPs, with polarization function by definition), or CEP41G plus my own optimized polarization function? Looking forward to hearing from you, Stefan Konietzny. From chemistry-request@server.ccl.net Mon Jan 8 07:33:04 2001 Received: from oz.che.rochester.edu (janeou@[128.151.211.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08CX4p03994 for ; Mon, 8 Jan 2001 07:33:04 -0500 Received: (from janeou@localhost) by oz.che.rochester.edu (8.9.3/8.9.3) id HAA24493 for chemistry@ccl.net; Mon, 8 Jan 2001 07:31:29 -0500 (EST) Date: Mon, 8 Jan 2001 07:31:29 -0500 (EST) From: Jane-Jane Ou Message-Id: <200101081231.HAA24493@oz.che.rochester.edu> To: chemistry@ccl.net Subject: Molecular Simulation Programs Hi, Which molecular simulation program can best predict the helical structure of a molecule? Thanks. Jane From chemistry-request@server.ccl.net Mon Jan 8 09:27:08 2001 Received: from hawk.dcu.ie (mail.dcu.ie [136.206.1.5]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08ER7p04378 for ; Mon, 8 Jan 2001 09:27:08 -0500 Received: from dcu.ie (136.206.86.63) by hawk.dcu.ie (5.1.050) id 3A3F6BC30002949D for chemistry@ccl.net; Mon, 8 Jan 2001 14:26:27 +0000 Message-ID: <3A59CE22.CAF6C891@dcu.ie> Date: Mon, 08 Jan 2001 14:26:43 +0000 From: Dermot Brougham X-Mailer: Mozilla 4.73 [en] (Win98; I) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: molecular modelling workshop Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi, I am currently applying for funding to run a workshop in molecular modelling for our 4th year group (40 students). I plan to give 4-5 lectures and then have a series of workshops (maybe 4x3 hours) with progressively less supervision as time goes on. Ending up with the students picking a problem of their own (probably from their organic chemistry lectures) and tackling it using whatever methods they see as fit and then writing a short report. Maybe the people who read the CCL have done something similar. I would be grateful for any advice, particularly about: Software: Best? Value for money? Hardware: Do you need a PC each or can you have them in pairs, threes....? Pedagogy: Has there been much published on this type of course? What are the major issues? Does the course I have outlined make pedagogical sense? Or is there a superior alternative approach? PS. We will be using PC’s with Windows98. -Sorry Jan if this is a little off-topic!!! Dermot -- Dr. Dermot Brougham, School of Chemical Sciences, Dublin City University, Dublin 9, Ireland. Tel: 353 1 7005472 Fax: 353 1 7005503 From chemistry-request@server.ccl.net Mon Jan 8 13:14:18 2001 Received: from ucidoor.unitedcatalysts.com ([208.23.162.2]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08IEIp05531 for ; Mon, 8 Jan 2001 13:14:18 -0500 Received: by ucidoor.unitedcatalysts.com; (8.8.8/1.3/10May95) id NAA32403; Mon, 8 Jan 2001 13:12:55 -0500 (EST) Received: from 10.1.0.50 by ucismtp02.unitedcatalysts.com (InterScan E-Mail VirusWall NT); Mon, 08 Jan 2001 13:13:02 -0500 (Eastern Standard Time) Received: from lvlxch01.unitedcatalysts.com ([10.16.100.88]) by lvlmail.unitedcatalysts.com (PMDF V6.0-24 #41777) with ESMTP id <0G6U0062SVRAXR@lvlmail.unitedcatalysts.com> for chemistry@ccl.net; Mon, 08 Jan 2001 13:09:10 -0500 (EST) Received: by lvlxch01.unitedcatalysts.com with Internet Mail Service (5.5.2650.21) id ; Mon, 08 Jan 2001 13:12:10 -0500 Content-return: allowed Date: Mon, 08 Jan 2001 13:12:00 -0500 From: "Shobe, Dave" Subject: PC Gamess orbital viewer To: "'CCL'" Message-id: <157A51F55AAAD3119CD70008C7B1629DDAABAD@lvlxch01.unitedcatalysts.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2650.21) Content-type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id f08IEIp05532 I'm afraid I'll need some more help with Gamess. An important step in multi-reference calculations is the selection of orbitals to include in the active space. In Gaussian the command is guess=(read,alter), but in Gamess I gather that one simply reorders the orbitals in the $VEC group. The problem is that I don't have an orbital viewer for Gamess. The PC Gamess homepage http://quantum-2.chem.msu.ru/gran/gamess/index.html basically says "we don't have one either"--although at least it explained why example 9 in the Gamess manual (a CAS calculation of H2O) didn't work as printed. But surely someone here has one(?) It's not absolutely necessary but would make things much easier. --David Shobe Süd-Chemie Inc. phone (502) 634-7409 fax (502) 634-7724 email dshobe@sud-chemieinc.com From chemistry-request@server.ccl.net Mon Jan 8 15:02:20 2001 Received: from canter-n-siegel.schrodinger.com (canter-n-siegel.schrodinger.com [192.156.98.248]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08K2Kp05802 for ; Mon, 8 Jan 2001 15:02:20 -0500 Received: (from info@localhost) by canter-n-siegel.schrodinger.com (8.8.5/8.8.5) id MAA31865 for chemistry@ccl.net; Mon, 8 Jan 2001 12:02:19 -0800 From: Schrodinger Info account Message-Id: <200101082002.MAA31865@canter-n-siegel.schrodinger.com> Subject: ANNC: Schrodinger Releases MacroModel 7.1 To: chemistry@ccl.net Date: Mon, 8 Jan 2001 12:02:19 -0800 (PST) X-Mailer: ELM [version 2.5 PL0b2] MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Schrodinger, Inc. announces that it is now shipping MacroModel 7.1, the latest version of the well-known molecular modeling package. The new release of MacroModel introduces new features and includes improvements in performance over previous versions. In addition, this version of MacroModel ships with Maestro 3.0, the latest release of Schrodinger's unified graphical user interface. Maestro is a powerful molecular building tool that produces structure files which are compatible with Schrodinger's MacroModel, Jaguar and Impact. Maestro facilitates tandem use of these products by acting as a hub through which each of the programs can be accessed and operated. MacroModel and Maestro run on all common hardware platforms, including SGI, IBM, HP, Compaq, Sun and Linux. For more information, please visit our website www.schrodinger.com. From chemistry-request@server.ccl.net Mon Jan 8 16:34:04 2001 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.11.0/8.11.0) with SMTP id f08LY4p06127 for ; Mon, 8 Jan 2001 16:34:04 -0500 Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 862569CE.0075FAFA ; Mon, 8 Jan 2001 15:28:39 -0600 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu To: chemistry@ccl.net cc: jolsenho@cosmos.dsc.unomaha.edu Message-ID: <862569CE.0075F9D2.00@unomail.unomaha.edu> Date: Mon, 8 Jan 2001 15:28:34 -0600 Subject: Quick question on G98 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCl'ers, In Gaussian when one assigns the amount of memory and the number of processor in the link0 input area, is the memory requested for each processor? In other works if I assign %mem=16 and %NProc=4 will the job use a total of 16X4=48 MW, or just 16 MW total? Thanks in advance, Douglas E. Stack Assistant Professor Department of Chemistry University of Nebraska at Omaha Omaha, NE 68182-0109 (402) 554-3647 (402) 554-3888 (fax) destack@unomaha.edu From chemistry-request@server.ccl.net Mon Jan 8 16:13:49 2001 Received: from mr.usu.edu (mr.usu.edu [129.123.1.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08LDnp06095 for ; Mon, 8 Jan 2001 16:13:49 -0500 Received: from tapaskar (tapaskar.chem.usu.edu [129.123.3.37]) by mr.usu.edu (Postfix) with SMTP id 8C4D91D374 for ; Mon, 8 Jan 2001 13:51:51 -0700 (MST) Message-ID: <000e01c079b4$9aaff1b0$25037b81@tapaskar> From: "Tapas Kar" To: "CCL" Subject: Molpro installation problem Date: Mon, 8 Jan 2001 13:50:16 -0700 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_000B_01C07979.EE4029C0" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4133.2400 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4133.2400 This is a multi-part message in MIME format. ------=_NextPart_000_000B_01C07979.EE4029C0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Molpro-experts, I got the following error while installing MOLPRO2000.1 in our = XP1000/TrueUnix4.0F. There was no error to ./configure. What's the problem here and how to = solve this? Thanks, Tapas # make Multiple rules lines for `licence.o' Make: Don't know how to make ../lib/libmolpro.a. Stop. *** Exit 1 Stop. _______________________________________ Tapas Kar, Ph.D Department of Chemistry & Biochemistry Utah State University 0300 Old Main Hill Logan, UT 84322-0300 Voice: 435-797-7230 Fax: 435-797-3390 Email: tapaskar@cc.usu.edu tapas@risky3.chem.usu.edu ----------------------------------------- ------=_NextPart_000_000B_01C07979.EE4029C0 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Molpro-experts,
I got the following error while = installing=20 MOLPRO2000.1 in our XP1000/TrueUnix4.0F.
There was no error to ./configure. = What's the=20 problem here and how to solve this?
Thanks,
Tapas
 
# make
 
Multiple rules lines for = `licence.o'
Make: Don't=20 know how to make ../lib/libmolpro.a.  Stop.
*** Exit=20 1
Stop.
 
_______________________________________
 
Tapas Kar, Ph.D
Department of = Chemistry &=20 Biochemistry
Utah State University
0300 Old Main Hill
Logan, UT = 84322-0300
 
Voice: 435-797-7230
Fax:   = 435-797-3390
Email: tapaskar@cc.usu.edu
 &nbs= p;    =20 tapas@risky3.chem.usu.edu
 
-----------------------------------------
------=_NextPart_000_000B_01C07979.EE4029C0-- From chemistry-request@server.ccl.net Mon Jan 8 16:15:40 2001 Received: from chala.q1.fcen.uba.ar (chala.q1.fcen.uba.ar [157.92.31.25]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08LFcp06107 for ; Mon, 8 Jan 2001 16:15:38 -0500 Received: from localhost (damian@localhost) by chala.q1.fcen.uba.ar (8.9.3/8.9.3) with ESMTP id TAA03462 for ; Mon, 8 Jan 2001 19:56:16 +0100 Date: Mon, 8 Jan 2001 19:56:16 +0100 (MET) From: =?X-UNKNOWN?Q?Dami=E1n_Scherlis?= To: chemistry@ccl.net Subject: ONIOM/AMBER in Gaussian Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, I have done some test calculations using the ONIOM method (Gaussian98) to combine DFT with either AM1 or AMBER. I assumed that the ONIOM procedure will solve the High and Low regions of the system in a self consistent way, so that the electron density of one part is affected by the density of the other. Instead I noticed that the energy of the High and Low layers did not depend on each other, as if each subsystem were isolated. As you see, I have probably a wrong idea of what ONIOM is, or I can't manage to interpret the results. I will appreciate any comment to clarify this question. Let me ask another question: when I try to run AMBER the computation is interrupted with the following message, though I included all atom types in the input: Stretching parameters undefined for 1 (O ) - 2 (O ) Stretching parameters undefined for 3 (HC) - 6 (CC) Stretching parameters undefined for 4 (CW) - 10 (HC) Stretching parameters undefined for 5 (CR) - 11 (HC) Bending parameters undefined for 3 (HC) - 6 (CC) - 4 (CW) Bending parameters undefined for 3 (HC) - 6 (CC) - 7 (NA) Bending parameters undefined for 6 (CC) - 4 (CW) - 10 (HC) Bending parameters undefined for 7 (NA) - 5 (CR) - 11 (HC) Bending parameters undefined for 8 (NA) - 4 (CW) - 10 (HC) Bending parameters undefined for 8 (NA) - 5 (CR) - 11 (HC) Not enough parameters to run AMBER Error termination via Lnk1e in /usr/bin/g98/l402.exe. Should I provide all these parameters in an additional file? How is this done? Thanks in advance -- Damian Scherlis Department of Physical Chemistry Faculty of Sciences University of Buenos Aires From chemistry-request@server.ccl.net Mon Jan 8 17:08:48 2001 Received: from blackadder.cis.McMaster.CA (blackadder.CIS.McMaster.CA [130.113.128.1]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08M8mp06336 for ; Mon, 8 Jan 2001 17:08:48 -0500 Received: from mcmaster.ca (opus.Chemistry.McMaster.CA [130.113.108.24]) by blackadder.cis.McMaster.CA with ESMTP id RAA25382 for ; Mon, 8 Jan 2001 17:08:46 -0500 (EST) Sender: jenkins@blackadder.cis.McMaster.CA Message-ID: <3A5A3A6D.2962CAAA@mcmaster.ca> Date: Mon, 08 Jan 2001 17:08:45 -0500 From: Samantha Jenkins Organization: McMaster University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: Maestro X-Priority: 1 (Highest) References: <200101082002.MAA31865@canter-n-siegel.schrodinger.com> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Can Maestro handle periodic unit cells, edit them and export them? From chemistry-request@server.ccl.net Mon Jan 8 18:15:30 2001 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08NFUp06733 for ; Mon, 8 Jan 2001 18:15:30 -0500 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id SAA25821; Mon, 8 Jan 2001 18:15:30 -0500 (EST) Message-ID: <041801c079c9$5519de80$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: =?iso-8859-1?Q?Dami=E1n_Scherlis?= Cc: "CCL - all" References: Subject: Re: CCL:ONIOM/AMBER in Gaussian Date: Mon, 8 Jan 2001 18:18:38 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Damian, ONIOM works by calculating the whole molecule at the low level. Then the high-level zone is saturated with hydrogens and calculated at both the high and the low level. The final energy is: E(low,all) - E(low,part) + E(high,part) There is a paper by Stefan Dapprich et al explaining all this in detail. It is about three or four years old. Yours, Stefan ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Mon Jan 8 19:12:45 2001 Received: from jaguar.it.wsu.edu (root@jaguar.it.wsu.edu [134.121.0.73]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f090Cjp06896 for ; Mon, 8 Jan 2001 19:12:45 -0500 Received: from ucis (ucis.chem.wsu.edu [134.121.41.180]) by jaguar.it.wsu.edu (8.9.3/8.9.3) with SMTP id QAA21218; Mon, 8 Jan 2001 16:12:44 -0800 (PST) Message-ID: <002201c079d0$e0f53a60$b4297986@chem.wsu.edu> From: "Phillip D. Matz" To: , Cc: References: <862569CE.0075F9D2.00@unomail.unomaha.edu> Subject: Re: CCL:Quick question on G98 Date: Mon, 8 Jan 2001 16:12:39 -0800 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.3018.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.3018.1300 Hello Dr. Stack, The answer is that the %mem link0 command specifies the total non-coherent memory size accessible virtually or physically. For a Unified Memory Architecture (UMA) system the system's memory is coherent and each processor will have access to all of the system memory. Thus, 16MW on a 4-way system with UMA will access a total of 16MW. However, for computer systems that employ Non-Unified Memory Architectures (NUMA) the system's memory is not coherent. In this case each processor is assigned a portion of the total system memory and no other processor can access the information stored in that memory (thus the designation NUMA). NUMA systems can be logically or physically partitioned. A cluster of workstations or Beowulfs typically have NUMA as the memory is stored on each motherboard and is accessible only by the cpus physically connected by a northbridge (in x86 land) to the memory. In this case specifying 16MW will result in the use of 48MW for four processors, but since it is NUMA the job itself will appear to be using only 16MW. So the answer is that the gaussian job will believe it is occupying a memory footprint that is the size specified by the Link0 %mem command (16MW in your example), but in the real world it may or may not be tying up more physical memory depending on the UMA vs NUMA for your particular system. A rule of thumb is that physically separated processors access memory in NUMA style (COWS, NOWS, and Beowulfs), while integrated workstations (SP2s, CRAYs, Alphas, Sparcs, etc...) access in UMA style. As a personal example, my cluster has roughly 1.5GB total, but it is NUMA and my G98 jobs are ran using only about 70MB. If it was UMA I could run G98 jobs employing all 1.5GB (great for in-core jobs!)... Respectfully, Phillip Matz matz@wsunix.wsu.edu ----- Original Message ----- From: To: Cc: Sent: Monday, January 08, 2001 1:28 PM Subject: CCL:Quick question on G98 > Dear CCl'ers, > > In Gaussian when one assigns the amount of memory and the number of processor in > the link0 input area, is the memory requested for each processor? In other > works if I assign %mem=16 and %NProc=4 will the job use a total of 16X4=48 MW, > or just 16 MW total? > > Thanks in advance, > > Douglas E. Stack > Assistant Professor > Department of Chemistry > University of Nebraska at Omaha > Omaha, NE 68182-0109 > (402) 554-3647 > (402) 554-3888 (fax) > destack@unomaha.edu > > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon Jan 8 18:08:59 2001 Received: from qtp.ufl.edu (zwart.qtp.ufl.edu [128.227.89.3]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f08N8wp06720 for ; Mon, 8 Jan 2001 18:08:58 -0500 Received: from pc1 (pc1 [128.227.192.187]) by qtp.ufl.edu (8.9.1a/8.9.1) with SMTP id SAA25770; Mon, 8 Jan 2001 18:09:25 -0500 (EST) Message-ID: <040f01c079c8$7b924ee0$bbc0e380@qtp.ufl.edu> From: "Stefan Fau" To: "Stefan Konietzny" Cc: "CCL - all" References: <01010514402700.01598@koronium> Subject: =?iso-8859-1?Q?Re:_CCL:Question_about_ECP=B4s_and_Basis_Sets?= Date: Mon, 8 Jan 2001 18:12:33 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2314.1300 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2314.1300 Hi Stefan, generally the Stuttgart-Dresden ECP basis sets do not include polarization functions. The ECP basis sets of very heavy elements are an exception. Look at e.g. the basis sets for the halogens. Also, G9x does not have a set of polarization functions to add to the (usually) DZ valence basis sets. To Q1: A good question! It is usually difficult to optimize exponents of ECP valence basis sets with respect to the energy. The exponents tend to get very large, meaning that the function is used to describe core electrons which should be described by the ECP only. Still, it might work for polarization functions. The Stuttgart-Dresden ECPs are optimized with respect to excitation and ionization energies of atoms. That is unambiguous. Optimizing molecular energies is probably better, but there are a few problems: * The choice of molecules is not unambiguous and might influence the result. * You might need to optimize the geometries for each basis set. * It definitely takes longer than just calculating atoms. Have a look at the papers of Stoll, Preuss et al. I think there is a paper of M. Kaupp et al that suggests a reparametrization of the halogen basis sets based on results for some earth- alkali-dihalides. That might be of interest with respect to the "atom or molecules" question. To Q2: You do not need to use ECPs everywhere. It is sufficient to use balanced valence basis set, as you suggested. The Stuttgart-Dresden ECP basis sets use different exponents for s- and p-functions. 6-31G* and related basis sets use identical exponents (sp shells). This speeds up the AO-integral evaluation at the cost of slightly worse basis set performance. It might be better to use basis sets with individual s- and p- exponents like Ahlrichs SVP, cc-pVDZ and many more. Yours, Stefan (too) ______________________________________________________________________ Dr. Stefan Fau | fau@qtp.ufl.edu Quantum Theory Project | (352) 392-6714 University of Florida Gainesville, FL 32611-8435 From chemistry-request@server.ccl.net Mon Jan 8 20:59:10 2001 Received: from schrodinger.com (root@thermidore.schrodinger.com [192.156.98.99]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f091xAp07016 for ; Mon, 8 Jan 2001 20:59:10 -0500 Received: from tandoori.schrodinger.com (root@tandoori.schrodinger.com [216.216.237.99]) by schrodinger.com (8.8.5/8.8.5) with ESMTP id RAA24270; Mon, 8 Jan 2001 17:59:07 -0800 Received: from sally.schrodinger.com (shenkin@sally.schrodinger.com [216.216.237.92]) by tandoori.schrodinger.com (8.8.5/8.8.5) with ESMTP id UAA03881; Mon, 8 Jan 2001 20:59:02 -0500 Received: from localhost (shenkin@localhost) by sally.schrodinger.com (8.8.8/8.8.5) with ESMTP id VAA03706; Mon, 8 Jan 2001 21:00:11 -0500 X-Authentication-Warning: sally.schrodinger.com: shenkin owned process doing -bs Date: Mon, 8 Jan 2001 21:00:11 -0500 (EST) From: Peter Shenkin To: Samantha Jenkins cc: chemistry@ccl.net Subject: Re: CCL:Maestro In-Reply-To: <3A5A3A6D.2962CAAA@mcmaster.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi, Samantha, Our Maestro GUI does not do this right now; however, we hope this month or next to set up Maestro for use for explicit-solvent simulations with periodic conditions in the Impact program. At that point, we'll have to do something about this, but I'm not sure whether it will be done at the level of the Impact input file or the level of the Maestro structure file. This will be limited to cubic lattices for liquid simulations, AFAIK. I'm not sure whether you're in fact asking for full crystallographic symmetry. We don't have any immediate plans to implement the latter. Hope this helps, -P. On Mon, 8 Jan 2001, Samantha Jenkins wrote: > > Can Maestro handle periodic unit cells, edit them and export them? > > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net > > > > > From chemistry-request@server.ccl.net Mon Jan 8 22:14:31 2001 Received: from fep3.online.sh.cn ([202.96.209.76]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f093EUp07110 for ; Mon, 8 Jan 2001 22:14:30 -0500 Received: from cadd ([61.129.166.212]) by fep3.online.sh.cn (InterMail vM.4.01.03.00 201-229-121) with SMTP id <20010109031448.IAJP26026.fep3.online.sh.cn@cadd> for ; Tue, 9 Jan 2001 11:14:48 +0800 Date: Tue, 9 Jan 2001 11:17:4 +0800 From: To: "chemistry@ccl.net" Subject: summary of IR software Organization: School of pharmacy, second military medical university X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20010109031448.IAJP26026.fep3.online.sh.cn@cadd> Dear sir, Here is a summary of responses. Thanks to all who responded. My original question is as follows: > I need to have a free IR software to read a IR spectrum file. > However, I didn't have one at hand.Does anyone can tell me > where I can get a free software? Dr.P.Verwer advice: ------------------------------------------------------------ See http://www.mdli.com/cgi/dynamic/welcome.html Hope this helps, Paul Verwer. -- Dr. P. Verwer CMBI A3023-a University of Nijmegen Phone: +31 (0)24 3653369 P.O. Box 9010 Fax: +31 (0)24 3652977 6500 GL Nijmegen verwer@cmbi.kun.nl The Netherlands http://www.cmbi.kun.nl/staff/verwer.html ============================================================================= Advanced Chemistry Development offers free SpecViewer 4.5, which, when installed with free ChemSketch 4.5 allows the viewing, processing, and report editing for MS, NMR, UVIR/Raman Spectra. Input formats available are JCAMP, ASCII (*.txt), Galactic (*.spc) and ACD (*.esp) formats. Free download is available at www.acdlabs.com/download The software is licensed for home or educational use only. If you are an industrial user, you must obtain a commercial license. For more information about our commercial IR software, please visit: http://www.acdlabs.com/products/spec_lab/exp_spectra/uv_ir/ Many thanks, Gavin Also ,someone adviced me to use Irplus program,which may be useful. But I didn't tried. Thanks to those who responsed to my question From chemistry-request@server.ccl.net Mon Jan 8 22:14:43 2001 Received: from fep2.online.sh.cn ([202.96.209.75]) by server.ccl.net (8.11.0/8.11.0) with ESMTP id f093Ehp07122 for ; Mon, 8 Jan 2001 22:14:43 -0500 Received: from cadd ([61.129.166.212]) by fep2.online.sh.cn (InterMail vM.4.01.03.00 201-229-121) with SMTP id <20010109031504.HGUI19118.fep2.online.sh.cn@cadd>; Tue, 9 Jan 2001 11:15:04 +0800 Date: Tue, 9 Jan 2001 11:17:20 +0800 From: To: "chemistry@ccl.net" CC: "asmasomy@mum.mans.eun.eg" Subject: summary Organization: School of pharmacy, second military medical university X-mailer: FoxMail 2.1 [cn] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: <20010109031504.HGUI19118.fep2.online.sh.cn@cadd> Dear sir, Here is a summary of responses. Thanks to all who responded. My original question is as follows: **************************************************************************** I am making research of IR properties of camptothecin by quantum chemical methods.I wonder if any of you can supply me with a picture of infrared spectrum of camptothecin? Can you tell me any free resources that includes IR spectrum? Thank you in advance! **************************************************************************** Although I didn't find the IR spectrum of camptothecin,I did received some useful information,I will put them here: -------------------------------------------------------------------------- Mr.Dragoe gave his addvice: Please check http://www.aist.go.jp/NIMC/nimcdb-e.html I am not sure they have your compound there but this free database contains quite a lot of info. Cheers, http://www.chem.t.u-tokyo.ac.jp/appchem/labs/kitazawa/dragoe/ -------------------------------------------------------------------------- Mr.Sara Matinez Check out this book: "FT-NIR Atlas" by Buback and Vogele (1993). There you can find spectra by molecular formula or name. Thanks to all those who responsed to my problem. Song Yunlong,PhD