From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Friday, October 31, 1997 9:20 AM To: hyperchem@hyper.com Subject: ChemPlus x.x and Amber 5.0 <3.0.32.19971031112027.00a1c8b0@mbi.ucla.edu> MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BCE616.ABB3FD60" Sender: listadmin@hyper.com Precedence: bulk Reply-To: Laurence Lavelle Hi, HyperChem recently announced various "good deals" for HyperChem and HyperNMR. Is there also a price reduction for current HC 5.02 users who purchase Chemplus x.x? Also what is the current version of ChemPlus? Also an update as to when (if?) Amber 5.0 will be integrated into HyperChem would be helpful for current users to "plan ahead". Thanks Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: jsalb@ix.netcom.com Sent: Friday, October 31, 1997 9:18 PM To: hyperchem@hyper.com Cc: LAVELLE@MBI.UCLA.EDU Subject: Re: ChemPlus x.x and Amber 5.0 Laurence, There are numerous bugs in the latest version of ChemPlus, especially in its interaction with HyperChem 5.02 running under NT. Despite repeated bug reports to Hypercube over many months, these bugs have not been fixed. Jesse On Fri, 31 Oct 1997 14:20:27 -0500 X-Priority: 3 X-MS-TNEF-Correlator:, you wrote: ><3.0.32.19971031112027.00a1c8b0@mbi.ucla.edu> > MIME-Version: 1.0 > X-Mailer: Internet Mail Service (5.0.1457.3) > Content-Type: multipart/mixed; > boundary="---- =_NextPart_000_01BCE616.ABB3FD60" >Sender: listadmin@hyper.com >Precedence: bulk >Reply-To: Laurence Lavelle > > >Hi, >HyperChem recently announced various "good deals" for HyperChem and >HyperNMR. Is there also a price reduction for current HC 5.02 users who >purchase Chemplus x.x? >Also what is the current version of ChemPlus? >Also an update as to when (if?) Amber 5.0 will be integrated into >HyperChem would be helpful for current users to "plan ahead". > >Thanks >Laurence Lavelle > > >""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" " >"""""""""""""""""""" >Laurence Lavelle, Ph.D. >University of California Los Angeles >Molecular Biology Institute, and Department of Chemistry & Biochemistry > >Laboratory of Structural Biology & Molecular Medicine >Los Angeles, CA 90095-1570, USA > >Email:LAVELLE@MBI.UCLA.EDU >Phone (Lab): (310) 206-8270 >Phone (Office): (310) 825-2083 >Fax: (310) 267-1957 >http://www.mbi.ucla.edu/people/lavelle/lavelle.html >""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" " >"""""""""""""""""""" > >It will be a great day when schools have all the money they need, >and the military has bake day sales. > > > >In nature's infinite book of secrecy >A little I can read. > From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Saturday, November 01, 1997 7:54 AM To: 'hyperchem@hyper.com' Subject: RE: ChemPlus x.x and Amber 5.0 I usually do not bother answering non-specific comments like the one just posted by Jesse Salb - every software has bugs in it, even HyperChem and ChemPlus! We are doing our best to detect, analyze and remove such features from our software. For the most recent list of bug fixes in HyperChem 5.02, please see our Web page at www.hyper.com/support/software/updates/hyperchem5/501to502.htm Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: jsalb@ix.netcom.com Sent: Saturday, November 01, 1997 11:15 AM To: hyperchem@hyper.com Subject: Re: ChemPlus x.x and Amber 5.0 On Sat, 1 Nov 1997 07:54:11 -0500, you wrote: >I usually do not bother answering non-specific comments like the one >just posted by Jesse Salb - every software has bugs in it, even >HyperChem >and ChemPlus! We are doing our best to detect, analyze and remove such >features from our software. > >For the most recent list of bug fixes in HyperChem 5.02, please see our >Web page >at www.hyper.com/support/software/updates/hyperchem5/501to502.htm The original poster did not ask about bugs in HyperChem. He asked about ChemPlus. Where on your web site is the list of bug fixes for ChemPlus? Jesse From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Saturday, November 01, 1997 12:23 PM To: 'hyperchem@hyper.com' Subject: Re: ChemPlus x.x and Amber 5.0 The original posting of Dr. Lavelle asks for a pricing info and the latest version of ChemPlus (1.6); these issues will be addressed directly by our Sales Department. We post regularly press releases for the latest products and updates we have, including bug fixes, to the newsgroup and on our Web site at www.hyper.com. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Sunday, November 02, 1997 10:22 PM To: hyperchem@hyper.com Subject: INCREASING CPU UTILIZATION WITH NT4 This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------ =_NextPart_000_01BCE7DD.3DE49330 Content-Type: text/plain HI, I HAVE A DUAL PENTIUM 133MHZ WITH NT4 WORKSTATION RUNNING VERY CPU INTENSIVE CALCULATIONS (AB INITIO IN HYPERCHEM 5.02) FROM DAYS TO WEEKS IN DURATION. 196 MB RAM 5GB VIRTUAL MEMORY (ALL SCSI HD'S WITH A SUSTAINED DATA TRANSFER RATE OF 10MB/S.) (The machine could be upgraded to dual 200MMX.) HOWEVER TASK MANAGER SHOWS CPU UTILIZATION AT A CONSTANT 54%. ONLY WHEN I USE OTHER ADDITIONAL SOFTWARE DOES THE CPU UTILIZATION GO ABOVE 54% AND UP TO 100%. HOW DO I OBTAIN HIGHER (100% ?) CPU UTILIZATION WITH ONLY THE COMPUTATIONAL SOFTWARE RUNNING? THANKS IN ADVANCED. LAURENCE LAVELLE """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. 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Since your mail reader does not understand this format, some or all of this message may not be legible. ------ =_NextPart_000_01BCE7E3.CC2EE8B0 Content-Type: text/plain Hi, Just remembered that Task Manager was showing the average of the two CPU's. After showing each CPU activity I realized what I already knew. HyperChem is a single thread application and no matter how many CPU's there are only one is used by HC. So one CPU is working 100% and totally dedicated to HC while the second CPU is dealing with the small OS overhead (~8%), giving an average CPU utilization of 54%. Of course when I use other software the second CPU is then utilized. Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. 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This was helpful to both the HyperCube support people and the users, because detailed, quantitative answers could be maintain in the database and reused or added to when similar support questions were asked. Why does HyperCube no longer use this mutually beneficial approach? Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: listadmin@hyper.com Sent: Friday, November 07, 1997 9:52 AM Subject: Ab Initio calculations <3.0.32.19971106132323.00a17c10@mbi.ucla.edu> MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BCEACF.ADF2C670" Sender: listadmin@hyper.com HyperChem Users, Since my ab initio calculations are taking longer than I expected, I decided to benchmark HyperChem 5.01 and HyperChem 5.02 to determine if one was faster than another (better optimized). Everything else is the same: OS, computer, computational settings within HyerChem. Using Propane as the test molecule the results are: MM+(Molecular Mechanics) HC 5.01 37sec HC 5.02 21sec PM3(Semi-Empirical) HC 5.01 2min 35sec HC 5.02 2min 6sec Ab Initio using STO-3G HC 5.01 1min 21sec HC 5.02 1min 4sec Yes, HyperCube did improve HyperChem's speed with Version 5.02. If anyone has benchmarks that differ from the above statement, please let me know. Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: listadmin@hyper.com Sent: Friday, November 07, 1997 10:14 AM Subject: RE: Maximizing the use of your archives The support archives of Hypercube are located at www.hyper.com/support. They include Frequently Asked Questions, Newsgroup and Software archives. Building a searchable database on the Web using these archives is a current project of Hypercube and will be implemented on our Web site in the future. ---- Original Message---- From: Laurence Lavelle To: hyperchem@hyper.com Subject: Maximizing the use of your archives Date: Wed, 5.Nov.1997.22:06:30.-0500.X-Priority:3.X-MS-TNEF-Correlator:@hyper.com Apparently-To: hyperchem-list@ftp.hyper.com <3.0.32.19971105190630.00a19b80@mbi.ucla.edu> MIME-Version: 1.0 X-Mailer: Internet Mail Service (5.0.1457.3) Content-Type: multipart/mixed; boundary="---- =_NextPart_000_01BCEA36.78339030" Sender: listadmin@hyper.com Precedence: bulk Reply-To: Laurence Lavelle To: hyperchem@hyper.com Subject: Maximizing the use of your archives Date: Wed, 5 Nov 1997 22:06:30 -0500 X-Priority: 3 X-MS-TNEF-Correlator: This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------ =_NextPart_000_01BCEA36.78339030 Content-Type: text/plain HyperCube used to archive its support Questions & Answers. This was helpful to both the HyperCube support people and the users, because detailed, quantitative answers could be maintain in the database and reused or added to when similar support questions were asked. Why does HyperCube no longer use this mutually beneficial approach? Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: listadmin@hyper.com Sent: Friday, November 07, 1997 10:14 AM Subject: RE: Maximizing the use of your archives The support archives of Hypercube are located at www.hyper.com/support. They include Frequently Asked Questions, Newsgroup and Software archives. Building a searchable database on the Web using these archives is a current project of Hypercube and will be implemented on our Web site in the future. ---- Original Message---- From: Laurence Lavelle To: hyperchem@hyper.com Subject: Maximizing the use of your archives Date: Wed, 5.Nov.1997.22: 06:30.-0500.X-Priority:3.X-MS-TNEF-Correlator:@hyper.com Apparently-To: hyperchem-list@ftp.hyper.com HyperCube used to archive its support Questions & Answers. This was helpful to both the HyperCube support people and the users, because detailed, quantitative answers could be maintain in the database and reused or added to when similar support questions were asked. Why does HyperCube no longer use this mutually beneficial approach? Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: Miguel Moreno Carretero [mmoreno@ujaen.es] Sent: Monday, November 10, 1997 3:45 AM To: listadmin@hyper.com; cem@listserv.hyper.com Subject: New direction Dear Sir, My new e-mail is mmoreno@piturda.ujaen.es Sincerely yours, --------------------------------------------- Prof. Dr. Miguel N. Moreno Carretero Dep. Química Inorgánica y Orgánica Campus Universitario "Las Lagunillas" (ed. 5) Universidad de Jaén 23071-JAEN Tlf. 34 53 212150 Fax. 34 53 212186 --------------------------------------------- From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Friday, November 07, 1997 9:40 PM To: jsalb@ix.netcom.com; hyperchem@hyper.com Subject: Re: HyperChem benchmarks Hi Jesse and HC users, Since both sets of calculations were done exactly the same I did not include all computational details. However, with respect to the molecular mechanics: Propane Default MM+, using bond dipoles and no cutoffs. Polak Ribiere, Energy minimized using a Gr set to 1e-5 in vacuo. The hardware is: [Originally an AT&T Globalyst 730, Class 3358] OS WindowsNT* 4.0(SP3) NCR BIOS Version 1.06.00 (3358), 05/19/97 Dual Intel Pentium 133MHz (HC only uses one CPU) AUGUSTA Motherboard with VLSI 590 Chip Set 256KB, PB-SRAM L2 Cache 192MB, 60ns Parity DRAM (Seimans & Micron) Integrated S3 Vision968, 4MB VRAM, True Color (32-bit), 1024 by 768, 100Hz Refresh Frequency Integrated 16 bit stereo (Ensoniq Sound Scape 688) Integrated AMD PCSCSI Fast SCSI-2 controller Asante EtherPac 2000+ Ethernet Adapter Drive A: Internal 1.44MB FD Drive C: Internal Seagate ST-32107W, Fast-Wide SCSI-2, 7200RPM, 2.1GB, 512KB buffer Drive D: Internal Seagate Barracuda 2LP(ST-32550N), Fast SCSI-2, 7200RPM, 2.1GB, 512KB buffer Drive E: Internal Quantum Fireball, Ultra SCSI-3, 4500RPM, 3.2GB, 128KB buffer Drive F: Internal Conner Tape Drive, Fast SCSI-2, 4GB Drive G: Internal Matsushita CD-ROM (CR-508), 24X, Fast SCSI-2, 512 KB buffer Hope that helps. Laurence Lavelle At 11:03 AM 11/7/97 -0800, you wrote: >Laurence, > >Thanks for the very informative comparison benchmark. Could you please >describe the hardware configuration, and the MM+ algorithm and >gradient? > >Jesse > >On Fri, 7 Nov 1997 09:52:25 -0500, you wrote: > >> HyperChem Users, >> >> Since my ab initio calculations are taking longer than I >>expected, I decided to benchmark HyperChem 5.01 and HyperChem 5.02 to >>determine if one was faster than another (better optimized). >> Everything else is the same: OS, computer, computational >>settings within HyerChem. >> Using Propane as the test molecule the results are: >> MM+(Molecular Mechanics) >> HC 5.01 37sec >> HC 5.02 21sec >> >> PM3(Semi-Empirical) >> HC 5.01 2min 35sec >> HC 5.02 2min 6sec >> >> Ab Initio using STO-3G >> HC 5.01 1min 21sec >> HC 5.02 1min 4sec >> >> Yes, HyperCube did improve HyperChem's speed with Version 5.02. >> If anyone has benchmarks that differ from the above statement, >>please let me know. >> Laurence Lavelle >> > > > """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Saturday, November 08, 1997 9:38 PM To: hyperchem@hyper.com Subject: HyperChem Benchmarks HyperChem Users, Since I have received email indicating benchmarks that differ from mine, please check the version number and the paths before comparing HC 5.02 (which I found to be the best optimized), HC 5.01, HC 4.0, HC 3.0. Make a special note that the paths for the version that is open do in fact point to the directories of the open version and not to a different version. I also recommend you download the latest patches for each version prior to running your benchmark. I appreciate benchmark results that have been sent to me. However, since this is clearly a topic of interest to all HyperChem users please post them to the user group as others my have suggestions, including tech support. Thanks Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Sunday, November 09, 1997 9:48 PM To: hyperchem@hyper.com Subject: patches and updates for HC 5.02 Are there any current or soon to be released (30 days) patches and updates for HC 5.02 that I should be aware of. Thanks Laurence Lavelle From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Saturday, November 08, 1997 10:05 PM To: hyperchem@hyper.com; chemistry@infomeister.osc.edu Subject: Improving ab initio computational speed Two possible ways to speed up ab initio calculations are: 1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. 2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). Do either of these approaches have potential downfalls. Is one approach better than the other? Thanks Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: listadmin@hyper.com Sent: Monday, November 10, 1997 11:41 AM To: hyperchem@hyper.com Subject: Gradients obtained from ab initio calcs Received: from ftp.hyper.com by pp200.hyper.com with SMTP (Microsoft Exchange Internet Mail Service Version 5.0.1457.7) id V06790Q4; Mon, 10 Nov 1997 09:38:42 -0500 Received: (from majordom@localhost) by ftp.hyper.com (8.6.12/8.6.12) id JAA24950 for hyperchem-list; Mon, 10 Nov 1997 09:29:57 -0500 Message-Id: <199711101429.JAA24950@ftp.hyper.com> From: "Fabri Marsicano" Organization: Mintek To: hyperchem@hyper.com Subject: Gradients obtained from ab initio calcs Date: Mon, 10 Nov 1997 16:41:11 GMT+2 Sender: Reply-To: "Fabri Marsicano" Reply-To: "Fabri Marsicano" Organization: Mintek The following query is addressed to anyone out there who has used the Hyperchem ab initio functionality, and who has some background and experience with ab initio calculations. I have recently been using Hyperchem to perform ab initio calculations on various simple 1:1 complexes of Ni(2+) and Co(2+). I have been using STO-nG* basis sets (n=3-6) for all atoms. These are the only basis sets currently available on Hyperchem V5 that cover the first row transition elements. I am using geometry optimisations (without MP2 electron correlation calcs) to predict complex geometries, metal ion-donor atom bond lengths, etc., and have been using single point calculations (including MP2 electron correlations) to calculate energies of the final geometry-optimised structures. I am becoming a little confused about the meaning of the gradients obtained from these calculations. The geometry optimisations (with MP2 switched off) are performed to a target gradient of 0.15 kcal/mol/A. When I then proceed to do a single point calculation (with MP2 switched on) the gradient obtained from that calculation differs from (and is often much larger than) the target gradient of 0.15 used in the geometry optimisation. (It could, for arguments sake, have a value of 20). What really surprises me though is that if, after doing the single point calculation, I then proceed to re-minimise the energy of the molecule starting from the previously optimised structure (now with MP2 switched off of course), the starting gradient takes on the value (say 20) obtained from the previous single point calculation. This does not make sense to me. I would have thought that the gradient obtained for a particular structure with use of a particular basis set, should be a function only of the coordinates of the atomic nuclei, not of whether or not one has just carried out a single point calculation on that structure. If anyone out there could shed some light on the situation, I would really be most grateful. FABRI MARSICANO Dept. of Chemistry, University of the Witwatersrand, Johannesburg, South Africa. From: RSTOLOW@PEARL.TUFTS.EDU Sent: Monday, November 10, 1997 12:09 PM To: listadmin@hyper.com Subject: Change of address Please change my e-mail address from: rstolow@pearl.tufts.edu to: rstolow@emerald.tufts.edu Thanks for your help. Prof. Robert Stolow Department of Chemistry Tufts University Medford, MA 02155 From: Support [support@hyper.com] Sent: Monday, November 10, 1997 11:54 AM To: 'hyperchem@hyper.com' Subject: News server Starting early this month we have introduced a NNTP news server at news.hyper.com. Initially, we will post there messages that are published on the hyperchem@hyper.com listserver. In order to use it, you need to point your NNTP news client to news.hyper.com using, for example, Free Agent 1.1, a freeware downloadable from www.shareware.com and other download places. Intended postings to the news server should be sent again to hyperchem@hyper.com listserver and will then be resubmitted by the Hypercube staff to the archive section of the news server. The listserver at hyper.com belongs to a small, private network server which sends messages to a select group of subscribed recipients worldwide. Therefore, we discourage its usage for e-mail inquiries and private correspondence. Very large messages, or such containing sizable images should also be avoided. Please be concise and address problems that are sound, constructive and relevant to the HyperChem audience. The newsgroup is monitored to avoid sending out junk mail, spam, and indecent material to the world. Personal attacks and destructive flaming, or material that is clearly irrelevant to the newsgroup, will also be rejected. To try and avoid any sense that we are censuring this newsgroup, which is certainly not our intent, bounced messages will be made available online at our news server, news.hyper.com. From: Stavrev, Krassimir Sent: Monday, November 10, 1997 12:16 PM To: 'RSTOLOW@PEARL.TUFTS.EDU' Subject: RE: Change of address Done! Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: RSTOLOW@PEARL.TUFTS.EDU [SMTP:RSTOLOW@PEARL.TUFTS.EDU] Sent: Monday, November 10, 1997 12:09 PM To: listadmin@hyper.com Subject: Change of address Please change my e-mail address from: rstolow@pearl.tufts.edu to: rstolow@emerald.tufts.edu Thanks for your help. Prof. Robert Stolow Department of Chemistry Tufts University Medford, MA 02155 From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Monday, November 10, 1997 12:25 PM To: 'fabri@mpc.mintek.ac.za' Cc: 'hyperchem@hyper.com' Subject: RE: Gradients obtained from ab initio calcs Fabri: It could well be that the SCF convergence limit in your calculations is high; for transition-metal systems I would try 0.0001 kcal/mol, or lower, if affordable. This will give you a good density matrix to step on during the gradient minimization. If your SCF convergence limit is too high, the gradients could be unreliable and there may be a different starting basis for the gradient estimates - during the optimization the program utilizes the matrix from the previous step, while in a single-point calculation you basically start from scratch, or initial guess. This may result in (big) differences in the gradients from the geometry optimization and the single point in ab-initio or semiempirical calculations. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: "Fabri Marsicano" Organization: Mintek To: hyperchem@hyper.com Subject: Gradients obtained from ab initio calcs Date: Mon, 10 Nov 1997 16:41:11 GMT+2 Sender: Reply-To: "Fabri Marsicano" Reply-To: "Fabri Marsicano" Organization: Mintek The following query is addressed to anyone out there who has used the Hyperchem ab initio functionality, and who has some background and experience with ab initio calculations. I have recently been using Hyperchem to perform ab initio calculations on various simple 1:1 complexes of Ni(2+) and Co(2+). I have been using STO-nG* basis sets (n=3-6) for all atoms. These are the only basis sets currently available on Hyperchem V5 that cover the first row transition elements. I am using geometry optimisations (without MP2 electron correlation calcs) to predict complex geometries, metal ion-donor atom bond lengths, etc., and have been using single point calculations (including MP2 electron correlations) to calculate energies of the final geometry-optimised structures. I am becoming a little confused about the meaning of the gradients obtained from these calculations. The geometry optimisations (with MP2 switched off) are performed to a target gradient of 0.15 kcal/mol/A. When I then proceed to do a single point calculation (with MP2 switched on) the gradient obtained from that calculation differs from (and is often much larger than) the target gradient of 0.15 used in the geometry optimisation. (It could, for arguments sake, have a value of 20). What really surprises me though is that if, after doing the single point calculation, I then proceed to re-minimise the energy of the molecule starting from the previously optimised structure (now with MP2 switched off of course), the starting gradient takes on the value (say 20) obtained from the previous single point calculation. This does not make sense to me. I would have thought that the gradient obtained for a particular structure with use of a particular basis set, should be a function only of the coordinates of the atomic nuclei, not of whether or not one has just carried out a single point calculation on that structure. If anyone out there could shed some light on the situation, I would really be most grateful. FABRI MARSICANO Dept. of Chemistry, University of the Witwatersrand, Johannesburg, South Africa. From: samchay [jkraska@warren-wilson.edu] Sent: Monday, November 10, 1997 4:19 PM To: hyperchem@hyper.com Subject: torsional bond angle calculations Hello, my name is Jason Kraska. I am performing undergraduate research on molecular modelling using Hyperchem 4.0, Windows 95, and Excel 7.0. I am measuring the energy of ethane as one of its carbons is rotated. I am using a script i got off of the Hyperchem library of user information. My research hypothesis is that substituting a hydrogen on each carbon for {flourine, chlorine, bromine, or iodine) will progressively increase the systems total energy. Such was the case until i performed the calculation on 1,2-diiodoethane. It had a total energy that was actually lower than that of bromine. This result excites me and consequently i need a more efficient method of performing the calculation. I was wondering if anyone out there in Hyperchem land has an Excel macro that performs the same function and puts the data into a spreadsheet by means of a DDE connection. I tried to convert the script to a macro but lack the syntax and correct logic to write a macro in Excel involving a DDE connection. Any help in this area will be greatly appreciated. Thank you in advance, Jason Kraska , jkraska@warren-wilson.edu Her kisses left something to be desired----the rest of her. Cocaine is God's way of letting you know you have too much money. From: Fabri Marsicano [fabri@mpc.mintek.ac.za] Sent: Tuesday, November 11, 1997 3:45 AM To: stavrev@hyper.com Subject: RE: Gradients obtained from ab initio calcs > From: "Stavrev, Krassimir" > To: "'fabri@mpc.mintek.ac.za'" > Cc: "'hyperchem@hyper.com'" > Subject: RE: Gradients obtained from ab initio calcs > Date: Mon, 10 Nov 1997 12:24:48 -0500 > Reply-to: "Stavrev, Krassimir" Many thanks for your suggestion, Krassimir. I have been using an SCF convergence limit of 0.00001 kcal/mol. I shall try narrowing the SCF convergence limit further to see if this helps. I take your point that gradients obtained from optimisation and from single point calculations may differ, and your explanation for why this is so. What bothers me is that if one starts a re-optimisation after having carried out a single point calculation, the program seems to use the gradient obtained in the single point calculation as the gradient for the first point in the re-optimisation. Presumably this means that the program is using the density matrix calculated in the single point calculation as the first guess in the new optimisation sequence. Is this correct ? This seems an odd thing for the program to do, since the density matrix obtained in the single point calculation is presumably based on some considerations (i.e., electron correlation) additional to those normally involved in optimisation calculations. It would seem more logical for the new optimisation to to follow on directly from the point at which the old optimisation left off. On another tack - I have noticed that it seems far more difficult to obtain low final gradients for Co(II) [multiplicity=4] complexes than it is for the corresponding Ni(II) [multiplicity=3] complexes. Considerations of hardness/softness would lead one to expect the Co(II)-donor bonds to be more ionic (less covalent) than the corresponding Ni(II)-donor bonds in the systems we are studying. Could this be the source of our difficulties ? Does the ab-initio method cope well with compounds having bonds with a large degree of ionicity ? If not, do you know, offhand, of an approach that does better in this respect ? Regards, FABRI > Fabri: It could well be that the SCF convergence limit in your > calculations is high; for transition-metal systems I would try 0.0001 > kcal/mol, or lower, if affordable. This will give you a good density > matrix to step on during the gradient minimization. If your SCF > convergence limit is too high, the gradients could be unreliable and > there may be a different starting basis for the gradient estimates - > during the optimization the program utilizes the matrix from the > previous step, while in a single-point calculation you basically start > from scratch, or initial guess. This may result in (big) differences in > the gradients from the geometry optimization and the single point in > ab-initio or semiempirical calculations. > Regards, > Krassimir > --- > Krassimir Stavrev, PhD, Director of Scientific Support > Hypercube, Inc. Florida Science and Technology Park > 1115 N.W. 4th Street Gainesville, Florida 32601 > Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 > -----Original Message----- > From: "Fabri Marsicano" > > Organization: Mintek > To: hyperchem@hyper.com > Subject: Gradients obtained from ab > initio calcs > Date: Mon, 10 Nov 1997 16:41:11 GMT+2 > Sender: Reply-To: "Fabri Marsicano" > > Reply-To: "Fabri Marsicano" > Organization: Mintek > > > The following query is addressed to anyone out there who > has used the > Hyperchem ab initio functionality, and who has some > background and > experience with ab initio calculations. > I have recently been using Hyperchem to perform ab > initio calculations > on various simple 1:1 complexes of Ni(2+) and Co(2+). I > have been using > STO-nG* basis sets (n=3-6) for all atoms. These are the > only basis sets > currently available on Hyperchem V5 that cover the first > row transition > elements. I am using geometry optimisations (without MP2 > electron > correlation calcs) to predict complex geometries, metal > ion-donor atom > bond lengths, etc., and have been using single point > calculations > (including MP2 electron correlations) to calculate > energies of the final > geometry-optimised structures. > I am becoming a little confused about the meaning of the > gradients > obtained from these calculations. The geometry > optimisations (with MP2 > switched off) are performed to a target gradient of 0.15 > kcal/mol/A. > When I then proceed to do a single point calculation > (with MP2 switched > on) the gradient obtained from that calculation differs > from (and is > often much larger than) the target gradient of 0.15 used > in the geometry > optimisation. (It could, for arguments sake, have a > value of 20). What > really surprises me though is that if, after doing the > single point > calculation, I then proceed to re-minimise the energy of > the molecule > starting from the previously optimised structure (now > with MP2 switched > off of course), the starting gradient takes on the value (say > 20) > obtained from the previous single point calculation. > This does not make sense to me. I would have thought > that the gradient > obtained for a particular structure with use of a > particular basis set, > should be a function only of the coordinates of the > atomic nuclei, not > of whether or not one has just carried out a single > point calculation on > that structure. > If anyone out there could shed some light on the > situation, I would > really be most grateful. > FABRI MARSICANO > Dept. of Chemistry, > University of the Witwatersrand, > Johannesburg, > South Africa. > From: Birgit Grossmann [grossman@ruf.uni-freiburg.de] Sent: Tuesday, November 11, 1997 4:44 AM To: hyperchem@hyper.com Subject: Force constants for bending vibrations ? Hello. I wonder if I can get these out from AM1 calculations. The force constants of bonds are in the results, but these ones not IMO. Thanks in advance Birgit Grossmann From: Stavrev, Krassimir Sent: Tuesday, November 11, 1997 12:08 PM To: 'Birgit Grossmann' Subject: RE: Force constants for bending vibrations ? Birgit: I think this question was asked in the newsgroup before, we have also a FAQ on this subject with the following explanation. HyperChem reports a N * N force constant matrix that is obtained from the one the original 3N * 3N, with N being the number of atoms. A 3N * 3N force constant matrix can be very confusing so HyperChem, like MOPAC, gives an N * N force constant matrix describing the atom-atom interaction forces. This N * N force constant matrix is formed from the 3N * 3N force constant matrix by calculating the norm of the tensor of each atom. You may reconstruct the 3N * 3N force constant matrix from HyperChem log file output using the matrix equation: F C = C E where F is the mass-weighted force constant matrix (3N * 3N), C is the eigenvector (normal coordinate) matrix and E is the eigenvalue diagonal matrix. You can get C and E from the log file (with QuantumPrintLevel=9), and then you can calculate the matrix F by multiplying on the right by the inverse of C. The relationship between eigenvalue Ei in E and the vibrational frequency f is f = SQRT(Ei) / (2*PI*c) Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: Birgit Grossmann [SMTP:grossman@ruf.uni-freiburg.de] Sent: Tuesday, November 11, 1997 4:44 AM To: hyperchem@hyper.com Subject: Force constants for bending vibrations ? Hello. I wonder if I can get these out from AM1 calculations. The force constants of bonds are in the results, but these ones not IMO. Thanks in advance Birgit Grossmann From: Joel Polowin [joelp@agiss.com] Sent: Tuesday, November 11, 1997 12:57 PM To: hyper.com!hyperchem@gabriel.resudox.net Cc: 'Laurence Lavelle' Subject: RE: HyperChem benchmarks Laurence Lavelle wrote on Friday, November 07, 1997 9:39 PM: >>> Using Propane as the test molecule the results are: >>> MM+(Molecular Mechanics) >>> HC 5.01 37sec >>> HC 5.02 21sec >>> >>> PM3(Semi-Empirical) >>> HC 5.01 2min 35sec >>> HC 5.02 2min 6sec >>> >>> Ab Initio using STO-3G >>> HC 5.01 1min 21sec >>> HC 5.02 1min 4sec >>> >>> Yes, HyperCube did improve HyperChem's speed with Version 5.02. I am seeing very different results. I am running my calculations on a Pentium 90 (I think) with 32 MB RAM, under Windows 95. In all cases, calculation settings were the defaults from installation (Polak-Ribiere optimization, etc.) except as noted. My timing procedure was to use the following script: optim-max-cycles 2000 start-logging junk.log no menu-file-stop-log do-optimization start-logging junk.log yes menu-file-stop-log message "Done!" This gave me calculation times saved in the "junk.log" file accurate to one or two seconds. No software other than HyperChem and the usual background tasks of the operating system was running during my testing. HyperChem 5.01 was as installed from the CD; 5.02 was from the patch file dated October 16th on the Hypercube server, 2,604,274 bytes in size. Molecule and details HC 5.01 HC 5.02 diff time optim. in time optim. in time perhydroanthracene, model-built, AM1 2:49 21 cyc, 48 pt 5:03 21 cyc, 48 pt +79% Same, with Fletcher-Reeves optim. 3:17 23 55 5:42 23 55 +74% Same, eigenvector-follow. 3:12 19 38 5:02 19 38 +57% ATA nucleotides, MM+ 13:35 547 1715 21:42 531 1666 +60% Same, with AMBER 0:56 322 677 1:08 322 677 +21% ATCGA nucleotides, AMBER 2:45 467 970 3:36 491 1013 +31% AT nucleotides, MM+ 5:02 397 1328 6:53 360 1120 +37% AT nucleotides, MM+, Newton- Raphson optim., halted at 2000 cycles 8:43 12:58 +49% GLY-GLY, model-built, AM1 5:22 183 411 16:52 380 850 +214% ! propane, model-built, AM1 0:07 9 23 0:09 9 23 N/A GLY, model-built, AM1 0:13 16 39 0:14 16 39 N/A propane, model-built, STO-3G, direct SCF 22:02 12 34 20:23 12 34 * 7% GLY, model-built, STO-3G, direct SCF 26:34 18 45 20:15 18 45 * 24% In general, for most MM and SE calculations, there is a *significantly* poorer calculation speed with the patch than without it. This doesn't happen with the _ab initio_ calculations, at least not for the relatively small ones. It is clear that different paths along the potential energy hypersurface are followed by the different versions of HyperChem 5 -- in particular, see the GLY-GLY AM1 calculation above! -- and this suggests that something is not quite right with the optimizers. There is not good consistency in the numbers of cycles and points even for a single version of HyperChem optimizing the same structure several times in succession. (I repeated that rather startling GLY-GLY calculation several times, and it is essentially reproducible though the exact times and numers of cycles and points vary slightly.) Joel joelp@agiss.com From: russell white [rustler@charlotte.infi.net] Sent: Tuesday, November 11, 1997 6:23 PM To: hyperchem@hyper.com Subject: chemesthetics program, .cmd file import/export Hi, I have access to several molecular files created by a program called chemesthetics. The files all end in .cmd. There is a conversion program for converting these files to a format used by an animation program. Has anyone heard of this program? Is there any way to convert between this file format and HyperChem? Does anyone know where I can get a copy of the original program? Thanks for any help. Russell White rustler@charlotte.infi.net From: Stavrev, Krassimir Sent: Wednesday, November 12, 1997 10:06 AM To: 'russell white' Subject: RE: chemesthetics program, .cmd file import/export Russell: Have you tried Babel, see below - it may have it, or you may try to use the source code of Babel to write down your own filter tool to HyperChem's *.hin or other formats. --------- Babel 1.6 --------- You might find the shareware Babel 1.6 to be helpful in converting between various file formats. The following files are on joplin.biosci.arizona.edu/pub/Babel: babel-1.6.tar.Z -- unix sources and Makefile babel16.zip -- MS DOS executable; works also in Win95 DOS box Please remember to download these files by ftp'ing in binary mode (or set your web browser preferences accordingly). Windows 3.x and 95 versions of Babel 1.6 are also available from ftp.brunel.ac.uk/pc/chem, as babel16w and babelwin, respectively. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: russell white [SMTP:rustler@charlotte.infi.net] Sent: Tuesday, November 11, 1997 6:23 PM To: hyperchem@hyper.com Subject: chemesthetics program, .cmd file import/export Hi, I have access to several molecular files created by a program called chemesthetics. The files all end in .cmd. There is a conversion program for converting these files to a format used by an animation program. Has anyone heard of this program? Is there any way to convert between this file format and HyperChem? Does anyone know where I can get a copy of the original program? Thanks for any help. Russell White rustler@charlotte.infi.net From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Wednesday, November 12, 1997 1:15 PM To: hyperchem@hyper.com Subject: Improving ab initio computational speed On Nov 8 I posted the message below but have had no responses. If requested I will summarize and post replies that I receive. Two possible ways to speed up ab initio calculations are: 1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. 2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). Do either of these approaches have potential downfalls? Is one approach better than the other? Thanks Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Wednesday, November 12, 1997 2:44 PM To: 'Laurence Lavelle' Cc: 'hyperchem@hyper.com' Subject: RE: Improving ab initio computational speed Laurence: The first approach makes more sense to me; the second one may affect the accuracy of the calculations unpredictably. In any case, with HyperChem 5 one can only export the eigenvector matrix and reproduce properties when the matrix is imported back, but cannot use the ext-file to form an initial guess of the Fock matrix. Accordingly, the SCF information that is stored at certain point is lost when one proceeds with another single-point calculation. It would be nice to have such read-from-file initial guess option in the program; it would be especially useful for people who run lengthy calculations and want to restart the job from the point where the SCF procedure was terminated. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 -----Original Message----- From: Laurence Lavelle [SMTP:lavelle@mbi.ucla.edu] Sent: Wednesday, November 12, 1997 1:15 PM To: hyperchem@hyper.com Subject: Improving ab initio computational speed On Nov 8 I posted the message below but have had no responses. If requested I will summarize and post replies that I receive. Two possible ways to speed up ab initio calculations are: 1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. 2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). Do either of these approaches have potential downfalls? Is one approach better than the other? Thanks Laurence Lavelle """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" Laurence Lavelle, Ph.D. University of California Los Angeles Molecular Biology Institute, and Department of Chemistry & Biochemistry Laboratory of Structural Biology & Molecular Medicine Los Angeles, CA 90095-1570, USA Email:LAVELLE@MBI.UCLA.EDU Phone (Lab): (310) 206-8270 Phone (Office): (310) 825-2083 Fax: (310) 267-1957 http://www.doe-mbi.ucla.edu/people/lavelle/lavelle.html """""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""" """""""""""""""""""" It will be a great day when schools have all the money they need, and the military has bake day sales. In nature's infinite book of secrecy A little I can read. From: Eugene Fleischmann [gene@q-chem.com] Sent: Thursday, November 13, 1997 11:15 AM To: Laurence Lavelle Cc: hyperchem@hyper.com Subject: Re: Improving ab initio computational speed Laurence Lavelle wrote: > > On Nov 8 I posted the message below but have had no responses. > If requested I will summarize and post replies that I receive. > > Two possible ways to speed up ab initio calculations are: > 1) Use a bases set with fewer bases functions first. Then, after > convergence, use a bases set with more bases functions. Repeat > this process until convergence is obtained with the (largest) bases set > that was originally intended. > 2) Use the largest bases set with a higher 2e integral cuttoff > point > (e.g. 10^-7 Hartree) and after convergence decrease the 2e > integral > cuttoff point. Repeat until convergence is obtained with the > originally > intended 2e integral cuttoff point (e.g. 10^-11 Hartree). > > Do either of these approaches have potential downfalls? > Is one approach better than the other? > > Thanks > Laurence Lavelle > Sender: listadmin@hyper.com Precedence: bulk Reply-To: Eugene Fleischmann Unless your starting structure is really bad, I cannot recommend approach 1) above, as it is more efficient to start with the final basis set. The optimized structure and hessian from a run with a smaller basis set may be no better than a good initial guess at the initial structure on the original structure. Nevertheless, Q-Chem can handle such projections of a smaller basis onto a larger one. Regarding approach 2) above, it is more efficient to adjust the integral cutoff iteratively within the SCF scheme rather than stopping, reading, and restarting the job using multiple single point calculations. Such a variable cutoff approach is already being used by a number of programs, including Q-Chem. Best Wishes, Eugene Fleischmann -- +--------------------------------------------------------------------+ | Eugene D. Fleischmann, Ph.D. http://www.q-chem.com | | Director of Sales | | Q-Chem, Inc. voice: (609) 896-3942 | | 317 Whipple St. FAX: (609) 896-1244 | | Pittsburgh, PA 15218 email: gene@q-chem.com | +--------------------------------------------------------------------+ From: Laurence Lavelle [lavelle@mbi.ucla.edu] Sent: Monday, November 17, 1997 4:53 PM To: chemistry@infomeister.osc.edu; hyperchem@hyper.com Subject: Replies received: Improving ab initio computational speed Thanks for all the replies, they are listed below. (It appears that there was a 4 day delay from the time I posted my message to CCL.) My original question was: >Date: Sat, 08 Nov 1997 19:05:12 -0800 >To: hyperchem@hyper.com, chemistry@infomeister.osc.edu >From: Laurence Lavelle >Subject: Improving ab initio computational speed > >Two possible ways to speed up ab initio calculations are: > >1) Use a bases set with fewer bases functions first. Then, after convergence, use a bases set with more bases functions. Repeat this process until convergence is obtained with the (largest) bases set that was originally intended. > >2) Use the largest bases set with a higher 2e integral cuttoff point (e.g. 10^-7 Hartree) and after convergence decrease the 2e integral cuttoff point. Repeat until convergence is obtained with the originally intended 2e integral cuttoff point (e.g. 10^-11 Hartree). > >Do either of these approaches have potential downfalls. Is one approach better than the other? > >Thanks >Laurence Lavelle ************************************************************************ **** ****************** Date: Mon, 17 Nov 1997 14:03 -0600 From: "David Maxwell" To: lavelle@mbi.ucla.edu Subject: Re: Improving ab initio computational speed Dear Laurence, Both of the methods you listed may be utilized to achieve your goal of speeding up the calculations. When utilizing a lower basis set, be aware that there may not be a one-to-one correspondence of minima between different basis sets. With regards to the integral accuracy, I have only seen rare occasions where this became a problem and it was usually when I was working with elements further down on the periodic table. Something you may also want to try is optimizing with some geometrical values held fixed and then allowing them to relax in a follow-up calculation. Sincerely, Dave ************************************************************************ **** **************** Date: Fri, 14 Nov 97 09:47:22 -0330 From: jamesx@bohr.chem.mun.ca (James Xidos) To: LAVELLE@MBI.UCLA.EDU Subject: Geometry Optimisation The rate of convergence in a geometry optimisation is directly dependent on the quality of your initial guess, and the quality of your Hessian (force constant matrix). The best route, through experience, of optimising structures at higher basis sets is to first, optimise at a lower basis set, followed by evaluating the Hessian (force constant matrix) at that lower basis set, then input both geometry and Hessian into your higher basis set job. Your second suggestion could help speed up the calculation of the initial steps in your higher level geometry optimisation, but a good geometry and Hessian will eliminate steps. I would be more inclined to increase the SCF convergence criteria for the initial steps as opposed to manipulate the 2e integral cutoffs. James Xidos Memorial University of Newfoundland jamesx@bohr.chem.mun.ca ************************************************************************ **** **************** From: "Chris Murray" Date: Mon, 17 Nov 1997 17:17:45 +0000 To: lavelle@mbi.ucla.edu Subject: Improving ab initio computational speed Hi Laurence, I'm surprised you got no responses since I always imagine there is someone ready to answer this type of question. 1) Use a basis set with fewer bases functions first. You can do this but it involve some algebra unless the large basis set is just an augmented form of the first. I seem to remember the results are disappointing in going from STO-3G to 3-21G say. It did not seem to be better than forming a density matrix from a superposition of results from pre-stored isotropic density matrices for atoms in the correct basis set. Good references are: Almlof's original Direct SCF paper or Cremer and Gauss, J. Comp. Chem. Vol. 7, pp274 (1986). 2) My feeling about the 2e cutoff's is that it won't work well enough to justify doing it. Also if you are doing a Direct SCF and using a change in density matrix elements in the integral test then there is a danger of inhibiting converence - in such cases it is advisable to increase the tolerances slightly during the run. Hope that this is some help. chris ************************************************************************ **** **************** From: "Stavrev, Krassimir" To: "'Laurence Lavelle'" Cc: "'hyperchem@hyper.com'" Subject: RE: Improving ab initio computational speed Date: Wed, 12 Nov 1997 14:44:22 -0500 Sender: listadmin@hyper.com Reply-To: "Stavrev, Krassimir" Laurence: The first approach makes more sense to me; the second one may affect the accuracy of the calculations unpredictably. In any case, with HyperChem 5 one can only export the eigenvector matrix and reproduce properties when the matrix is imported back, but cannot use the ext-file to form an initial guess of the Fock matrix. Accordingly, the SCF information that is stored at certain point is lost when one proceeds with another single-point calculation. It would be nice to have such read-from-file initial guess option in the program; it would be especially useful for people who run lengthy calculations and want to restart the job from the point where the SCF procedure was terminated. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 ************************************************************************ **** **************** Sender: turner@ocisgi28.unizh.ch Date: Mon, 17 Nov 1997 09:03:08 +0100 From: Alexander J Turner Organization: OCI - University of Zurich To: Laurence Lavelle Subject: Re: CCL:Improving ab initio computational speed References: <3.0.32.19971108190512.00a2a3d0@mbi.ucla.edu> Hi! In reply to your question. Both methods have merit, but there are potential problems. The main problem with the basis function idea is that it assumes that a higher basis set calculation will converge faster from your low basis set optimized structure than from your original guess. This might well not be the case. It will tend to be the case much more if you compute an exact hessian at the low basis set end point and use that as the guess hessian for the higher basis set calculations. This can be especially so for HF -> MP2/DFT work. Also, you assume that the lower basis set will be able to model your compound at all. STO3G can be so far from 6-31g* (say) that your initial STO3G calculations 'lock' you into an unrealistic part of the potential energy surface. Such considerations are much more a problem when you are looking for transition states. The second method has a problem, it is virtually of no interest for conventional SCF. The time is taken computing the 2e integrals, not converging the SCF. For direct schemes, it is of interest, but only if you are going to try and get a very tight convergence of the SCF. I.E. so tight you encounter slight convergence problems. The normal property of convergence is that the last bit takes less time than the initial stages (because DIIS has more information to work with). Thus you gain little from the lower convergence, and that little you loose from the extra optimization cycles. So - my recommendation is inheritance of the structure _and_ hessian from a lower level of theory (or basis set) with extreme caution when applied to saddle points. Best wishes Alex ************************************************************************ **** **************** From: Eugene Fleischmann Organization: Q-Chem, Inc. To: Laurence Lavelle Cc: hyperchem@hyper.com Subject: Re: Improving ab initio computational speed Date: Thu, 13 Nov 1997 11:14:45 -0500 Unless your starting structure is really bad, I cannot recommend approach 1) above, as it is more efficient to start with the final basis set. The optimized structure and hessian from a run with a smaller basis set may be no better than a good initial guess at the initial structure on the original structure. Nevertheless, Q-Chem can handle such projections of a smaller basis onto a larger one. Regarding approach 2) above, it is more efficient to adjust the integral cutoff iteratively within the SCF scheme rather than stopping, reading, and restarting the job using multiple single point calculations. Such a variable cutoff approach is already being used by a number of programs, including Q-Chem. Best Wishes, Eugene Fleischmann ************************************************************************ **** ***************** From: Maciej Turowski [turek@farmacja.amg.gda.pl] Sent: Thursday, November 20, 1997 5:53 PM To: hyperchem@hyper.com Subject: Reactions by the force fields? Dear Hyperchemists, One question appeared during my presentations of HyperChem and I also would like to ask you about it: When simulating reactions by molecular dynamics - it should only be semi-empirical or ab-initio Hamiltonian used, shouldn=B4t be? I think there are no changing (breaking) bonds without electrons involved, because they (electrons) are the only bodies of chemical bonds. If so, then - why during MD using MM+ (!), and atomic charges option, there are changing chemical bonds (what only can be seen displaying by CPK-spheres)? When I give velocity of some atoms oriented at the certain molecules sometimes they replace those being there before "an attack". Is this logical only using Classical Mechanics, no electrons??? By the way - a question to Hypercube - why the CPK-sphere display uses only 2/3value of the Van der Waals radii??? It would be, = in my opinion, highly desirable to have full VdW radii of the atoms in display options. Even if it wouldn=B4t look so nice it was then MUCH, much more useful when interpreting results. Sometimes, in Structure-Activity analysis it is necessary. Best regards for all, make this list more vivid!!!! (or the reason that it so silent since a long time is that it became governed manually, = with a kind of censorship, I guess? Aren=B4t there just simple filtering devices for nasty words to automatize this list again and to make it more vivid?!?) Best regards again, Maciej Turowski, Ph.D. From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Friday, November 21, 1997 9:47 AM To: 'turek@farmacja.amg.gda.pl' Cc: 'hyperchem@hyper.com' Subject: RE: CPK Maciej: Hyperchem uses CPK (Corey, Pauling, Koltun) radii to construct the "Overlapping Spheres" display. CPK is a space-filling model which utilizes internal tables of atomic radii that are conveniently scaled (usually by a constant of 2/3) Van der Waals radii. Presently, one can change the CPK radii only via ChemPlus by editing the vdwgrid.txt file. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 From: Maciej Turowski [turek@farmacja.amg.gda.pl] Sent: Friday, November 21, 1997 12:06 PM To: Stavrev, Krassimir Cc: 'hyperchem@hyper.com' Subject: RE: CPK question Dear Krassimir, Thank you very much for your answer. Due to a fact that I am not able to look into my manuals (they're in Poland, I'm in Argentina now) I would like to ask you about an example of how to change the CPK radius via ChemPlus and whether it will be seen as a change in display in HyperChem screen (spheres)? Of course if it's not a trouble for you. Is there a good reference on CPK? Two things yet. First - about MM+ simulation of chemical reactions - it was my mistake because the simulations were set at semi-empirical options, indeed. Nevertheless, about some possible simulations by MM FF I've received one interesting e-mail already. Second - about the hyper-list. I haven't seen my own e-mail sent to me from the list-server. Why? In such case I'm not even sure whether it is placed there or not. Frankly said - I liked the form of the discussion list that was before the change (i.e. manual control) because there were much more activities seen. Isn't really possible to automatize the list again and to avoid some nasty e-mail just run a special filtering device? Thank you very much in advance, Maciej On Fri, 21 Nov 1997, Stavrev, Krassimir wrote: > Maciej: Hyperchem uses CPK (Corey, Pauling, Koltun) radii to construct > the "Overlapping Spheres" display. CPK is a space-filling model which > utilizes internal tables of atomic radii that are conveniently scaled > (usually by a constant of 2/3) Van der Waals radii. Presently, one can > change the CPK radii only via ChemPlus by editing the vdwgrid.txt file. > > Regards, > Krassimir > --- > Krassimir Stavrev, PhD, Director of Scientific Support > Hypercube, Inc. Florida Science and Technology Park > 1115 N.W. 4th Street Gainesville, Florida 32601 > Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662 > From: Stavrev, Krassimir [stavrev@hyper.com] Sent: Friday, November 21, 1997 1:19 PM To: 'Maciej Turowski' Cc: 'hyperchem@hyper.com' Subject: RE: CPK-addition One more place where you can access the CPK radii directly (using ChemPlus) is the HCMP.ini file; look for CPKradii. Regards, Krassimir --- Krassimir Stavrev, PhD, Director of Scientific Support Hypercube, Inc. Florida Science and Technology Park 1115 N.W. 4th Street Gainesville, Florida 32601 Voice:(352) 371-7744/(800) 960-1871 Fax:(352) 371-3662