From chemistry-request@server.ccl.net Wed Oct 31 00:30:29 2001 Received: from smtp1.fas.harvard.edu (IDENT:root@[140.247.30.81]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9V5UTB09013 for ; Wed, 31 Oct 2001 00:30:29 -0500 Received: from luke2000 (roam161-35.student.harvard.edu [140.247.161.35]) by smtp1.fas.harvard.edu with SMTP id f9V5XWh04468; Wed, 31 Oct 2001 00:33:32 -0500 (EST) From: "Jason L. Douglas" To: Subject: RE: Gaussian calculation speed Date: Wed, 31 Oct 2001 00:33:39 -0500 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook IMO, Build 9.0.2416 (9.0.2911.0) X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 Importance: Normal In-Reply-To: I would imagine the I/O subsystem to be a serious determining performance factor with SCF calculations, unless you're doing direct SCF. I've had similar results between a Dell PIII 450 with a SCSI disk, and a Dell PIII 733 with ATA. I understand that with Linux systems, I/O speed can vary greatly on how you've setup the OS, but I'm not intimately familiar with Red Hat 6 or 7, so I can't offer any real suggestions there. I'm sure if you replaced the ATA drive with a single SCSI drive, or even a SCSI RAID array, coupled with a good SCSI adapter, you'd have a very fast system, utilizing more of the faster processing speed. Hope that helps! Jason Douglas From chemistry-request@server.ccl.net Wed Oct 31 03:33:40 2001 Received: from amiga.chemie.uni-konstanz.de ([134.34.112.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9V8XeB10658 for ; Wed, 31 Oct 2001 03:33:40 -0500 Received: (from jochen@localhost) by amiga.chemie.uni-konstanz.de (8.11.6/8.8.7) id f9V8bJm13033; Wed, 31 Oct 2001 09:37:19 +0100 From: Jochen Buehler Message-ID: <15327.47166.789008.425394@amiga.chemie.uni-konstanz.de> Date: Wed, 31 Oct 2001 09:37:18 +0100 (CET) To: "Elena Jakubikova" Cc: chemistry@ccl.net Subject: CCL:Gaussian calculation speed In-Reply-To: References: X-Mailer: VM 6.75 under 21.1 (patch 14) "Cuyahoga Valley" XEmacs Lucid Mime-Version: 1.0 (generated by tm-edit 1.7) Content-Type: text/plain; charset=US-ASCII Elena Jakubikova writes: > Dear CCLers, > > I have run one CISD calculation with a relatively large > basis set on CH4 molecule on 2 different computers. > Computer one is Dell 550MHz Pentium III, 512MB RAM > (100MHz SDRAM), 18 GB SCSI #1 Hard Drive, and Red Hat > Linux 6.0 operating system. Computer two is Millennia > 733MHz Pentium III, 770MB RAM (133MHz SDRAM), 27GB IDE > ATA-66 hard drive, and Red Hat Linux 7.0 operating > system. > To my big surprise the calculation was much faster on > Dell (job cpu time = 24 minutes 1.8 sec) than on > Millennia (job cpu time = 1 hour 4 minutes 18.6 > seconds). Seems like you are using PIO transfer mode on Millenia. What does the output of hdparm say? Because of the disk I/O required for the job the (always operating in DMA mode) SCSI system is faster. Regards, Jochen -- Jochen Buehler, Dipl.-Chem EMail: jochen@amiga.chemie.uni-konstanz.de AG Prof. Dr. Daltrozzo buehler@chemie.uni-konstanz.de Fachbereich Chemie Phone: +49-7531-882095 Universitaet Konstanz Fax: +49-7531-883043 78457 Konstanz, Germany From chemistry-request@server.ccl.net Wed Oct 31 02:44:26 2001 Received: from avogadro.kk.ttu.ee (qmailr@[193.40.253.225]) by server.ccl.net (8.11.6/8.11.0) with SMTP id f9V7iPB10234 for ; Wed, 31 Oct 2001 02:44:25 -0500 Received: (qmail 7262 invoked by uid 1000); 31 Oct 2001 07:47:29 -0000 Date: Wed, 31 Oct 2001 09:47:28 +0200 From: Toomas Tamm To: chemistry@ccl.net Subject: Re: CCL:Gaussian calculation speed Message-ID: <20011031094728.B6956@avogadro.kk.ttu.ee> References: Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Mailer: Mutt 0.95.3i In-Reply-To: ; from Jason L. Douglas on Wed, Oct 31, 2001 at 12:33:39AM -0500 On Wed, Oct 31, 2001 at 12:33:39AM -0500, Jason L. Douglas wrote: > I would imagine the I/O subsystem to be a serious determining performance > factor with SCF calculations, unless you're doing direct SCF. I've had > similar results between a Dell PIII 450 with a SCSI disk, and a Dell PIII > 733 with ATA. I understand that with Linux systems, I/O speed can vary > greatly on how you've setup the OS, but I'm not intimately familiar with Red > Hat 6 or 7, so I can't offer any real suggestions there. I'm sure if you > replaced the ATA drive with a single SCSI drive, or even a SCSI RAID array, > coupled with a good SCSI adapter, you'd have a very fast system, utilizing > more of the faster processing speed. Hope that helps! Indeed, several distributions of Linux do not turn on the ATA-66 (or ATA-100) support by default. One can make a quick test of disk speed (as root) with "hdparm -t /dev/hda" (or /dev/sda for SCSI). Results in 4-5 MB/sec range indicate that the ATA support is off. A modern disk should deliver around 20-30 MB/sec with ATA-66 or ATA-100. For serious benchmarking, a more advanced tool, e.g. "bonnie" is recommended. One can enable UDMA (ATA-66 / ATA-100) on IDE disks with "hdparm -d1 /dev/hda" or similar. Other flags such as -c1 or -m16 to hdparm may benefit as well, but may also lead to data loss, so proceed very carefully. Avoid the -X flag to hdparm: I have personally had a case of data loss with such setup. -- Toomas Tamm e-mail: tt-ccl@kky.ttu.ee Inorganic and General Chemistry voice: INT+372-620-2810 Tallinn Technical University fax: INT+372-620-2796 Ehitajate tee 5, EE-19086 Tallinn, Estonia http://www.kk.ttu.ee/toomas/ From chemistry-request@server.ccl.net Wed Oct 31 04:00:54 2001 Received: from mail1.rrz.Uni-Koeln.DE ([134.95.100.208]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9V90rB11022 for ; Wed, 31 Oct 2001 04:00:53 -0500 Received: from campfire.rrz.Uni-Koeln.DE (IDENT:39358@campfire.rrz.Uni-Koeln.DE [134.95.19.27]) by mail1.rrz.Uni-Koeln.DE (8.9.3/8.9.3) with ESMTP id KAA15427; Wed, 31 Oct 2001 10:03:55 +0100 (MET) Received: (from a0580@localhost) by campfire.rrz.Uni-Koeln.DE (8.9.1a/8.9.1) id KAA29638; Wed, 31 Oct 2001 10:03:53 +0100 (MET) Date: Wed, 31 Oct 2001 10:03:52 +0100 From: Lars Packschies To: chemistry@ccl.net Cc: Elena Jakubikova Subject: Re: CCL:Gaussian calculation speed Message-ID: <20011031100352.A16988@campfire.rrz.Uni-Koeln.DE> Mail-Followup-To: chemistry@ccl.net, Elena Jakubikova References: Mime-Version: 1.0 Content-Type: multipart/signed; micalg=pgp-sha1; protocol="application/pgp-signature"; boundary="ikeVEW9yuYc//A+q" Content-Disposition: inline In-Reply-To: User-Agent: Mutt/1.3.23i --ikeVEW9yuYc//A+q Content-Type: text/plain; charset=us-ascii Content-Disposition: inline Content-Transfer-Encoding: quoted-printable * Jason L. Douglas [011031 07:46]: > greatly on how you've setup the OS, but I'm not intimately familiar with = Red > Hat 6 or 7, so I can't offer any real suggestions there. I'm sure if you Dear Elena, Jason suggested that it may be the I/O-Subsystem. If it's the case it can be tuned:=20 When you type (as superuser) hdparm -tT /dev/hda (or whatever the device of the HD is) you should get something like /dev/hda: Timing buffer-cache reads: 128 MB in 1.26 seconds =3D101.59 MB/sec Timing buffered disk reads: 64 MB in 3.56 seconds =3D 17.98 MB/sec if your HD is set up using the correct DMA and PIO modes. If not, you get values like 30 MB/sec (buffer-cache reads) and 3 MB/sec (buffered disk reads) for example. The values above show the HD in my RH 7 System, and its not one of the fastest. To set up the drive with hdparm look at the options with hdparm -h. And be careful. I just switched on DMA and 32-bit I/O-Support. hdparm /dev/hda shows you how the HD is configured. "Newer" 2.4 kernels (and late 2.2? not sure) can be set up to use DMA if available (I think it is the default setting). If you have an older kernel that does not support 32 bit I/O-Support you should get a new one.=20 Good luck, Lars --ikeVEW9yuYc//A+q Content-Type: application/pgp-signature Content-Disposition: inline -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (SunOS) Comment: For info see http://www.gnupg.org iD8DBQE73754kRMt176/QQkRAiYoAKDrRX1tbHMN2ynbXUmJLuna902fKgCfd8b8 n5GzrzStsB/xxP4TFUrkhBE= =2kKG -----END PGP SIGNATURE----- --ikeVEW9yuYc//A+q-- From chemistry-request@server.ccl.net Wed Oct 31 08:52:14 2001 Received: from ned1.sims.nrc.ca ([132.246.108.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VDqEB15215 for ; Wed, 31 Oct 2001 08:52:14 -0500 Received: from localhost (ps@localhost) by ned1.sims.nrc.ca (8.8.8/8.8.8) with ESMTP id IAA28054; Wed, 31 Oct 2001 08:55:12 -0500 (EST) Date: Wed, 31 Oct 2001 08:55:12 -0500 From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii@nrc.ca To: Elena Jakubikova cc: chemistry@ccl.net Subject: Re: CCL:Gaussian calculation speed In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Tue, 30 Oct 2001, Elena Jakubikova wrote: > I tried to run top while running only this one > calculation and found out that during the extensive I/O > phase of calculation (l804,l913), there is a lot of CPU > used by the system on Millennia computer (at certain > moments its more than 90%), whereas in the case of Dell > computer almost all cpu is used by the user. Most likely, running: /sbin/hdparm -d 1 /dev/hdc # Or whatever your scratch disk # device is will improve results. You need to run this command as root, so ask your system administrator to do it for you (and to add the command to an appropriate startup file). To check how much difference it makes for I/O transfers, run /dev/hdparm -t /dev/hdc # Again, whatever your scratch disk is before and after turning on DMA. It is not uncommon to see an order of magnitude improvement in transfer speed, once DMA is turned on. Regards, Dr. Serguei Patchkovskii Tel: +1-(613)-991-2719 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii@nrc.ca Research Council Officer Steacie Institute for Molecular Sciences National Research Council Canada Room 2158, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@server.ccl.net Wed Oct 31 10:36:21 2001 Received: from rbadb1.RBACPXCLU.BAS.ROCHE.COM ([196.3.50.190]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VFaKB17045 for ; Wed, 31 Oct 2001 10:36:21 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KA5O91Q42896XB9P@Roche.COM> for chemistry@ccl.net; Wed, 31 Oct 2001 16:24:48 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KA5O8WQJXY9AMV8J@Roche.COM> for chemistry@ccl.net; Wed, 31 Oct 2001 16:24:40 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Wed, 31 Oct 2001 16:24:37 +0100 Content-return: allowed Date: Wed, 31 Oct 2001 16:24:32 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: Woodward-Fieser Rules To: chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA7E5@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 f9VFaLB17046 Dear Colleauges, Thank you for the answers (specially ArgousLab was interesting). Does anyone know a program for calculation (estimation) of maximum wavelengths of UV absorption (lambda-max) by using Woodward-Fieser Rules: http://www.chemistry.ccsu.edu/glagovich/teaching/472/uvvis/diene.html Best regards, András Borosy Basilea Pharmaceutica Ltd POB 3255, 65/316 4002 Basel tel: +41-61-6885469 fax: +41-61-6882139 www.basileapharma.com From chemistry-request@server.ccl.net Wed Oct 31 10:43:18 2001 Received: from rbadb2.rbacpxclu.bas.roche.com ([196.3.50.241]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VFhHB17171 for ; Wed, 31 Oct 2001 10:43:17 -0500 Received: from CONVERSION-DAEMON.Roche.COM by Roche.COM (PMDF V6.0-025 #47170) id <01KA5OXS27OW96WMA0@Roche.COM> for chemistry@ccl.net; Wed, 31 Oct 2001 16:44:44 +0100 Received: from rbamsemcn1.bas.roche.com (rbamsemcn1.bas.roche.com [145.245.211.139]) by Roche.COM (PMDF V6.0-025 #47170) with ESMTP id <01KA5OXO28BA9AMWKK@Roche.COM>; Wed, 31 Oct 2001 16:44:37 +0100 Received: by rbamsemcn1.bas.roche.com with Internet Mail Service (5.5.2653.19) id ; Wed, 31 Oct 2001 16:44:34 +0100 Content-return: allowed Date: Wed, 31 Oct 2001 16:44:29 +0100 From: "Borosy, Andras {Basi~Basel}" Subject: RE: continuum regression To: "'Christian.Pilger@bc.boehringer-ingelheim.com'" , chemistry@ccl.net Message-id: <5FBD82D1CB46D511AAEA0002A55C6F5202AAA7EB@rbamsem3.bas.roche.com> MIME-version: 1.0 X-Mailer: Internet Mail Service (5.5.2653.19) 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 f9VFhIB17172 Dear CCLers, > is anybody aware of software capable of what is called 'continuum > regression' for statistical analysis ? PLS_Toolbox 2.1 for Matlab www.eigenvector.com Regards, András Borosy Basilea Pharmaceutica Ltd POB 3255, 65/316 4002 Basel tel: +41-61-6885469 fax: +41-61-6882139 www.basileapharma.com From chemistry-request@server.ccl.net Wed Oct 31 11:01:23 2001 Received: from soul.helsinki.fi ([128.214.3.1]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VG1MB17498 for ; Wed, 31 Oct 2001 11:01:22 -0500 Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.9.3/8.9.3) with ESMTP id SAA12913 for ; Wed, 31 Oct 2001 18:04:26 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Wed, 31 Oct 2001 18:04:26 +0200 (EET) From: Mikael Johansson X-Sender: Reply-To: Mikael Johansson To: Subject: Winter School in Theoretical Chemistry 2001 (Helsinki) In-Reply-To: <20011031094728.B6956@avogadro.kk.ttu.ee> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello All! Our traditional series of Winter Schools in Theoretical Chemistry continues. See http://www.chem.helsinki.fi/Info/WinterSchool/ The topic of this year's school is CONDENSED PHASE DYNAMICS. Please register as soon as possible. The program is enclosed. It is also available on the web-site, where eventual changes will appear. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson@helsinki.fi Phone: +358-9-191 50185 FAX : +358-9-191 50169 ***************************************************************** **** **** **** Winter School in Theoretical Chemistry 2001 **** **** **** **** CONDENSED PHASE DYNAMICS **** **** **** ***************************************************************** TIME: 10-13 December, 2001. (Start at 10:00 on Monday) VENUE: Department of Chemistry, University of Helsinki, A.I. Virtasen aukio 1, Helsinki, Finland. LANGUAGE: English. LECTURERS: Dominik Marx (4 h) (Bochum): "Ab initio molecular dynamics: theory I,II" "Ab initio molecular dynamics: applications I,II" Alexander Nemukhin (5 h) (Moscow): "Construction of potential energy surfaces for modelling structure, spectra and dynamics in condensed phases with emphasis on DIM (Diatomics in Molecules)" Risto Nieminen (2h) (Espoo): "Linear and nonlinear response using time-dependent density-functional theory," "Multiscale modelling of anisotropic chemical etching" Kai Nordlund (2h) (Helsinki): Mechanism of bond-breaking induced erosion of amorphous hydrogenated carbon, with application to fusion reactors", "Recrystallization mechanism of semiconductors by electron-irradiation-induced bond breaking" Burkhard Schmidt (4h) (Berlin): "Condensed phase dynamics; quantum dynamics, quantum-classical methods (trajectories, Gauss-packets, surface-hopping, photodissociation)" PROGRAM: (version 1.0) Monday Tuesday Wednesday 09:15-10:00 Marx I Schmidt IV 10:00-10:30 Welcome Break Break 10:30-11:15 Nemukhin I Marx II Nieminen II 11:30-12:15 Nemukhin II Nemukhin III Marx III 12:15-13:30 Lunch & posters Lunch & posters Lunch & posters 13:30-14:15 Schmidt I Nemukhin IV Marx IV 14:15-14:45 Break Break Break 14:45-15:30 Schmidt II Schmidt III Nemukhin V 15:45-16:30 Nordlund I Nieminen I Nordlund II 16:30- Posters Comp. Chem. Departure Section Meeting Tuesday 16.30: Meeting of the Computational Chemistry Section in the Laboratory of Instruction in Swedish. CONTRIBUTED Any member of the School is welcome to put up PAPERS: a poster on the premises. PROCEEDINGS: None. LEVEL: Post-graduate and research, for scientists already involved in computational quantum chemistry. The course is obligatory for PhD-students within the LASKEMO grad school. This year the exam will be replaced by an essay. The course will give 2 credits. FEES: University students and staff: none. ADMISSION: The participants are requested to register by 15 November, 2001 to the address below. Note that MOLPROP members should contact Dage. Dr Juha Vaara, Department of Chemistry, P.O.Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland. Telephone: 358-9-191 50181. FAX: 358-9-191 50169. E-mail: jvaara@chem.helsinki.fi MOLPROP Dr Dage Sundholm, Department of Chemistry, P.O.Box 55 (A.I. Virtasen aukio 1), FIN-00014 University of Helsinki, Finland Telephone: 358-9-19150 176 FAX: 358-9-19150 169 Email: sundholm@chem.helsinki.fi From chemistry-request@server.ccl.net Wed Oct 31 11:13:34 2001 Received: from relay.uni-heidelberg.de ([129.206.100.212]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VGDYB17768 for ; Wed, 31 Oct 2001 11:13:34 -0500 Received: from fubini.pci.uni-heidelberg.de (fubini.pci.uni-heidelberg.de [129.206.21.240]) by relay.uni-heidelberg.de (8.10.2+Sun/8.10.2) with ESMTP id f9VGGbf16621; Wed, 31 Oct 2001 17:16:37 +0100 (MET) Received: from euklid (euklid.pci.uni-heidelberg.de [129.206.21.104]) by fubini.pci.uni-heidelberg.de (8.11.0/8.11.0/SuSE Linux 8.11.0-0.4) with SMTP id f9VGGWn15928; Wed, 31 Oct 2001 17:16:32 +0100 X-Authentication-Warning: fubini.pci.uni-heidelberg.de: Host euklid.pci.uni-heidelberg.de [129.206.21.104] claimed to be euklid Content-Type: text/plain; charset="iso-8859-1" From: Bernd Schubert To: Toomas Tamm , chemistry@ccl.net Subject: Re: CCL:Gaussian calculation speed Date: Wed, 31 Oct 2001 17:16:39 +0100 X-Mailer: KMail [version 1.2] References: <20011031094728.B6956@avogadro.kk.ttu.ee> In-Reply-To: <20011031094728.B6956@avogadro.kk.ttu.ee> MIME-Version: 1.0 Message-Id: <01103117163901.00822@euklid> Content-Transfer-Encoding: 8bit > One can enable UDMA (ATA-66 / ATA-100) on IDE disks with "hdparm -d1 > /dev/hda" or similar. Other flags such as -c1 or -m16 to hdparm may > benefit as well, but may also lead to data loss, so proceed very > carefully. Avoid the -X flag to hdparm: I have personally had a case > of data loss with such setup. But without the -X flag you only enable to use dma-1 --> with a maximum transferrate of 16 MB/s. Using the -X flag you enable Ultra-DMA (ATA-33 -- -X34, ATA-66 -- -X66, etc.). Bernd From chemistry-request@server.ccl.net Wed Oct 31 11:20:04 2001 Received: from mercury.chem.nwu.edu (fparnold@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VGK4B17915 for ; Wed, 31 Oct 2001 11:20:04 -0500 Received: from localhost (fparnold@localhost) by mercury.chem.nwu.edu (8.11.3/8.11.3) with ESMTP id f9VGN8713107 for ; Wed, 31 Oct 2001 10:23:08 -0600 (CST) Date: Wed, 31 Oct 2001 10:23:08 -0600 (CST) From: "Fred P. Arnold" X-X-Sender: To: Subject: Mixing levels of DFT theory. Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello, In the old days, one would run a HF geometry optimization and Hessian (for thermochemical properties), then do single-point runs at the HF geometry using MP(n) methods to get the single-point energy, and combine the two for reaction energetics. Does the same practice hold for DFT? Specifically, if you have a SVWN (LDA) optimized geometry and frequencies, will you get better energetics (product - reactant, ignoring transition states for the moment) if you use single-point BLYP(@SVWN Geom) + SVWN(Thermo), using SVWN all the way through but augmenting the basis set with polarization and/or diffuse functions, use CCSD or MP(n) for the single points and the SVWN frequencies, or it's not systematic enough to say. -Fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu From chemistry-request@server.ccl.net Wed Oct 31 11:37:16 2001 Received: from mail.chem.tamu.edu (IDENT:root@[165.91.176.8]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id f9VGbGB18227 for ; Wed, 31 Oct 2001 11:37:16 -0500 Received: from [165.91.177.32] (account yubofan HELO mail.chem.tamu.edu) by mail.chem.tamu.edu (CommuniGate Pro SMTP 3.5b3) with ESMTP id 620197 for CHEMISTRY@ccl.net; Wed, 31 Oct 2001 10:34:28 -0600 Sender: yubo@ccl.net Message-ID: <3BE02988.6A340C96@mail.chem.tamu.edu> Date: Wed, 31 Oct 2001 10:40:40 -0600 From: Yubo Fan Organization: Chemistry Department, Texas A&M University X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP28) X-Accept-Language: zh-CN, en MIME-Version: 1.0 To: CHEMISTRY@ccl.net Subject: GIF file with frequency animation Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from base64 to 8bit by server.ccl.net id f9VGbGB18228 Hi, Guassview and HyperChem can visualize vibrational modes calculated by G98, to my knowledge. But, they can't export the animations to any format that common programs, such as Windows MediaPlayer, can load. In fact, I want to create some animated GIF files for some frequencies. I mean if I can capture 4 or 5 pictures from Guassview or HyperChem's animation, these GIF files can be created correctly. Any advice? Thanks in advance Yubo -- ============================================================ Yubo Fan Email: yubofan@mail.chem.tamu.edu Department of Chemistry Tel: 1-979-845-7222 Texas A&M University College Station, TX 77843 ============================================================ From chemistry-request@server.ccl.net Wed Oct 31 22:11:05 2001 Received: from lithium.theochem.uni-duesseldorf.de (IDENT:root@[134.99.82.3]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id fA13B4B04031 for ; Wed, 31 Oct 2001 22:11:04 -0500 Received: from chlor.theochem.uni-duesseldorf.de (IDENT:root@chlor.theochem.uni-duesseldorf.de [134.99.76.131]) by lithium.theochem.uni-duesseldorf.de (8.11.1/8.11.1) with ESMTP id fA13E1831678; Thu, 1 Nov 2001 04:14:01 +0100 Received: from localhost (wibke@localhost) by chlor.theochem.uni-duesseldorf.de (8.11.1/8.11.1) with ESMTP id fA13E1b32281; Thu, 1 Nov 2001 04:14:02 +0100 X-Authentication-Warning: chlor.theochem.uni-duesseldorf.de: wibke owned process doing -bs Date: Thu, 1 Nov 2001 04:14:00 +0100 (CET) From: Wibke Sudholt To: CHEMISTRY@ccl.net Subject: Adding hydrogens Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello everybody, I am searching for free programs that are able to add hydrogens to a given xyz or pdb structure (organic molecule, protein). It would be great if one has some control over this process, e.g. at which atoms how many hydrogens are attached. Many thanks for every help! Wibke Sudholt University of California, San Diego