From chemistry-request@ccl.net Thu Oct 30 00:45:07 2003 Received: from brass.metals.hope.edu (brass.metals.hope.edu [198.110.98.36]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9U5iaLk018595 for ; Thu, 30 Oct 2003 00:44:36 -0500 Received: from hope.edu ([198.110.98.17]) by brass.metals.hope.edu (SAVSMTP 3.1.1.32) with SMTP id M2003103000402116734 for ; Thu, 30 Oct 2003 00:40:21 -0500 Received: from hope.edu [65.42.185.255] (matthew.zwier~at~hope.edu) by hope.edu; Thu, 30 Oct 2003 00:41:57 -0500 X-WM-Posted-At: hope.edu; Thu, 30 Oct 03 00:41:57 -0500 Message-ID: <3FA0A50E.7010202~at~hope.edu> Date: Thu, 30 Oct 2003 00:43:42 -0500 From: Matthew Zwier User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.4) Gecko/20030810 X-Accept-Language: en-us, en MIME-Version: 1.0 To: CHEMISTRY~at~ccl.net Subject: CCL: G98 solvent field self-energy = -Inf Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello CCL, I am performing CIS calculations in a spatially large (~100A) solvent field. G98 frequently reports that the self energy of the charges (and hence nuclear repulsion after point charges) is +/-inf or +/-nan. Sample output is below. What could be causing this? Matt Zwier matthew.zwier~at~hope.edu --- G98 output --- ==> gaff10-md01-cis-sto3g.com.2363.out <== Self energy of the charges = -inf MM energy of the charges = 0.0000000000 Nuclear-Charge attraction = 7.4635702759 132 basis functions 396 primitive gaussians 79 alpha electrons 79 beta electrons nuclear repulsion energy 178.6160302949 Hartrees. Nuclear repulsion after solvent point charges= -inf Hartrees. One-electron integrals computed using PRISM. NBasis= 132 RedAO= T NBF= 132 NBsUse= 132 1.00D-04 NBFU= 132 INDO Guess failed. Using Huckel. Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Keep R1 integrals in memory in canonical form, NReq= 39760540. Restarting incremental Fock formation. Restarting incremental Fock formation. Restarting incremental Fock formation. >>>>>>>>>> Convergence criterion not met. SCF Done: E(RHF) = -inf A.U. after 65 cycles Convg = 0.3972D-01 -V/T = inf S**2 = 0.0000 Convergence failure -- run terminated. Error termination via Lnk1e in /usr/local/g98/l502.exe. Job cpu time: 0 days 0 hours 5 minutes 56.4 seconds. File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 Chk= 1 Scr= 1 ==> gaff10-md01-cis-sto3g.com.2355.out <== XYZ= 95.0000 15.4920 95.2000 Q= -0.6497 A= 0.0000 R= 0.0000 C= 0.0000 XYZ= 58.0000 69.8890 18.2000 Q= 0.4215 A= 0.0000 R= 0.0000 C= 0.0000 Self energy of the charges = -nan MM energy of the charges = 0.0000000000 Nuclear-Charge attraction = -6.3361909572 132 basis functions 396 primitive gaussians 79 alpha electrons 79 beta electrons nuclear repulsion energy 230.5357166344 Hartrees. Nuclear repulsion after solvent point charges= -nan Hartrees. One-electron integrals computed using PRISM. NBasis= 132 RedAO= T NBF= 132 NBsUse= 132 1.00D-04 NBFU= 132 Projected INDO Guess. Requested convergence on RMS density matrix=1.00D-08 within 64 cycles. Requested convergence on MAX density matrix=1.00D-06. Keep R1 integrals in memory in canonical form, NReq= 39760540. Restarting incremental Fock formation. Restarting incremental Fock formation. SCF Done: E(RHF) = -nan A.U. after 58 cycles Convg = 0.8843D-08 -V/T = nan S**2 = 0.0000 Range of M.O.s used for correlation: 23 132 NBasis= 132 NAE= 79 NBE= 79 NFC= 22 NFV= 0 NROrb= 110 NOA= 57 NOB= 57 NVA= 53 NVB= 53 **** Fatal Problem: The smallest alpha delta epsilon is 0.45156774D-03 Error termination via Lnk1e in /usr/local/g98/l801.exe. Job cpu time: 0 days 0 hours 17 minutes 29.9 seconds. File lengths (MBytes): RWF= 19 Int= 0 D2E= 0 Chk= 1 Scr= 1 From jkl@ccl.net Thu Oct 30 11:23:41 2003 -0500 Return-Path: Reply-To: From: "Mark Thompson" To: chemistry/at/ccl.net Cc: Subject: RE: ArgusLab 4 question Date: Thu, 30 Oct 2003 08:23:34 -0800 Message-ID: <000e01c39f02$2a836130$271ae70c@planaria> Richard, Would you send me the structure file for your peptide? The error is almost certainly that the am1.prm file does not contain zinc parameters (though I'm sorry you received a cryptic exception message, and I'll look into cleaning that up). Also, ArgusLab4 is currently a beta1 release and still contains little (and big) irritations. Regarding a higher-level of theory, you have a couple of options. 1. You can try PM3 in ArgusLab; which does support Zn. 2. If you have Gaussian98 or Gaussian03 available, you can run it directly > from ArgusLab's Gaussian interface. 3. You can have ArgusLab save the Gaussian input file and you can run it on another machine. 4. You can save the molecule as an xyz, pdb, or mol file which can be read by a number of other academic and commercial packages. Please let me know if I can be of more help. Also, you might consider joining the ArgusLab user's group. It's another good place to find out about bug fixes, and solutions to issues that others have found. (Go to http://www.arguslab.com and click on "Users Group" button). If you have any other feedback, I'd like to hear about it. Feel free to send me email. The peptide builder is new and I'd be interested in hearing if you liked it or had any suggestions. Best regards, Mark Thompson *************************** Mark Thompson, PhD Planaria Software LLC PO Box 55207 Seattle, WA 98155 mark/at/arguslab.com http://www.arguslab.com *************************** -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request/at/ccl.net]On Behalf Of Richard Wood Sent: Wednesday, October 29, 2003 2:34 PM To: chemistry/at/ccl.net Subject: CCL:ArgusLab 4 question Hi all I have a molecule that I've built in ArgusLab4. It's a small peptide that has a Zinc in it. I have optimized it using the Universal Force Field (UFF). Is there a way that I can "convert" my file so that I can do an optimization using a higher level of theory? For example, if I try to do an AMI calculation, I get an error message saying, "Unrecognized exception caught in runCalcThread". Thanks in advance, Richard From chemistry-request@ccl.net Thu Oct 30 14:36:33 2003 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9UJa1Lj019498 for ; Thu, 30 Oct 2003 14:36:01 -0500 Received: from [128.175.138.90] ([128.175.138.90]) by copland.udel.edu (8.12.10/8.12.10) with ESMTP id h9UJa1bk009468 for ; Thu, 30 Oct 2003 14:36:01 -0500 (EST) Message-Id: <200310301936.h9UJa1bk009468^at^copland.udel.edu> X-Mailer: Microsoft Outlook Express Macintosh Edition - 4.5 (0410) Date: Thu, 30 Oct 2003 14:28:54 -0500 Subject: Re: Symmetry and Gaussian From: "Olga Dmitrenko" To: chemistry^at^ccl.net Mime-version: 1.0 X-Priority: 3 Content-type: text/plain; charset="US-ASCII" Content-transfer-encoding: 7bit X-Spam-Score: 0.8 SPAM_PHRASE_00_01 X-Scanned-By: MIMEDefang 2.37 X-Spam-Status: No, hits=0.0 required=7.0 tests=none version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) One obvious suggestion is to prepare Z-matrix input. It's a little time-consuming, but one may use GaussView Z-matrix editor which is very helpful. Olga * Olga Dmitrenko * Postdoctoral Fellow * Department of Chemistry and Biochemistry * University of Delaware, Newark * Delaware 19716, USA *Tel: (302) 831-0887 * Email: odmitr^at^udel.edu From chemistry-request@ccl.net Thu Oct 30 09:22:42 2003 Received: from relay.uni-heidelberg.de (relay.uni-heidelberg.de [129.206.100.212]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9UEMALj009010 for ; Thu, 30 Oct 2003 09:22:11 -0500 Received: from euklid.pci.uni-heidelberg.de (euklid.pci.uni-heidelberg.de [129.206.21.104]) by relay.uni-heidelberg.de (8.12.10/8.12.10) with ESMTP id h9UEM7aj018676; Thu, 30 Oct 2003 15:22:07 +0100 (MET) Received: from bernd by euklid.pci.uni-heidelberg.de with local (Exim 3.35 #1 (Debian)) id 1AFDgd-0006mq-00; Thu, 30 Oct 2003 15:22:07 +0100 From: Bernd Schubert To: "Raymond C. Fort Jr." , chemistry^at^ccl.net Subject: Re: CCL:Symmetry and Gaussian Date: Thu, 30 Oct 2003 15:22:06 +0100 User-Agent: KMail/1.5.3 References: <5.1.1.6.0.20031029095508.00a1d9e0^at^mail.maine.edu> In-Reply-To: <5.1.1.6.0.20031029095508.00a1d9e0^at^mail.maine.edu> MIME-Version: 1.0 Content-Type: Multipart/Mixed; boundary="Boundary-00=_O6Ro/okDKz/qBzn" Message-Id: <200310301522.06918.bernd-schubert^at^web.de> Sender: Bernd Schubert X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_KMAIL version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) --Boundary-00=_O6Ro/okDKz/qBzn Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Content-Disposition: inline On Wednesday 29 October 2003 15:58, Raymond C. Fort Jr. wrote: > I'm sure this has been asked before, but the list archives currently are > not very searchable. I've been running some optimizations of small > molecules with G98 (ethylene, formaldehyde; Cartesian input) to illustrate > use of the program to a class. The calculations fail rapidly with the > message that there has been a change in point group or standard > orientation. So far, the only way I can get a calculation to finish is to > turn off symmetry. I'd appreciate suggestions of alternatives. > > Ray Hello Raymond, about 2.5 years ago this has been discussed and a patch has been sent to th= e=20 list. Since I also patched our gaussian that way, I created a readme-file i= n=20 the gaussian-directory that contains some parts of that mail and the patch= =20 (see attachement). Hope it helps, Bernd =2D-=20 Bernd Schubert Physikalisch Chemisches Institut / Theoretische Chemie Universit=E4t Heidelberg INF 229 69120 Heidelberg e-mail: bernd.schubert^at^pci.uni-heidelberg.de --Boundary-00=_O6Ro/okDKz/qBzn Content-Type: text/plain; charset="iso-8859-1"; name="README.bernd" Content-Transfer-Encoding: 7bit Content-Disposition: attachment; filename="README.bernd" I (Bernd) modified the Link202 within the Subroutine Omega regarding to a suggestion posted on the CCL-mailling-list: Hi all, In fact, it is a read-write file error. Due to the symmetry increase, the amount of memory allocated for this rwf (579) is not sufficient. To correct this bug, if you have access to the source code, you can add the following lines in the link 202. In subroutine Omega, just before the line Call FileIO(1,-IRwNEq,InToWP(NOp2*NAtoms),NEqAtm,0) add CALL FILEIO(11,-IRWNEQ,LEN,NEqAtm,0) IF(LEN.NE.0) THEN LEN=INTOWP(NOP2*NATOMS)-LEN CALL FILEIO(20,-IRWNEQ,LEN,NEqAtm,0) ENDIF It adjusts the length of the rwf. The job you gave now works fine ... until it crashes because 20 optimization steps are not enough to achieve a verytight optimization job ! Nicolas --Boundary-00=_O6Ro/okDKz/qBzn-- From chemistry-request@ccl.net Thu Oct 30 11:26:33 2003 Received: from mx4.trentu.ca (mx4.trentu.ca [192.75.12.5]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9UGPxLj013205 for ; Thu, 30 Oct 2003 11:25:59 -0500 Received: (qmail 7283 invoked by uid 510); 30 Oct 2003 16:24:29 -0000 Received: from elewars)at(trentu.ca by mx4.trentu.ca by uid 501 with qmail-scanner-1.20rc3 (fsecure: 4.50/2111/. spamassassin: 2.55. Clear:RC:1:. Processed in 0.309426 secs); 30 Oct 2003 16:24:29 -0000 X-Qmail-Scanner-Mail-From: elewars)at(trentu.ca via mx4.trentu.ca X-Qmail-Scanner: 1.20rc3 (Clear:RC:1:. Processed in 0.309426 secs) Received: from unknown (HELO trentu.ca) (209.42.101.30) by mx4.trentu.ca with SMTP; 30 Oct 2003 16:24:28 -0000 Message-ID: <3FA13BF7.568129E6)at(trentu.ca> Date: Thu, 30 Oct 2003 11:27:36 -0500 From: elewars X-Mailer: Mozilla 4.79 [en] (WinNT; U) X-Accept-Language: en MIME-Version: 1.0 To: "Raymond C. Fort Jr." , chemistry)at(ccl.net Subject: Re: CCL:Symmetry and Gaussian References: <5.1.1.6.0.20031029095508.00a1d9e0)at(mail.maine.edu> Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.1 required=7.0 tests=EMAIL_ATTRIBUTION,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_MOZILLA_XM,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello, If you use input with the symmetry that the optimized product will have, you should not have this problem. For simple molecules one usually knows what this symmmetry will be, e.g. H2CO with C2v input should optimize smoothly within this sym to give a C2v output geometry. I don't know how you get your input geometries; maybe the problem lies there. Occasionally it's hard to get exactly the input sym you want; in those cases Sym=Loose (with Gaussian) may help, or you may be able to hand-edit a small Cartesian file to the exact sym it should have. One should always try to optimize within the maximum "expected" symmetry; the presence of imaginary frequencies will tell you if you have to repeat at a lower symmetry. EL ============= "Raymond C. Fort Jr." wrote: > I'm sure this has been asked before, but the list archives currently are > not very searchable. I've been running some optimizations of small > molecules with G98 (ethylene, formaldehyde; Cartesian input) to illustrate > use of the program to a class. The calculations fail rapidly with the > message that there has been a change in point group or standard > orientation. So far, the only way I can get a calculation to finish is to > turn off symmetry. I'd appreciate suggestions of alternatives. > > Ray > > Professor Ray Fort Jr. Voice: (207)-581-1180 > Department of Chemistry FAX: (207)-581-1191 > University of Maine EMail: rcfort)at(maine.edu > Orono, ME 04469 Web: > chemistry.umeche.maine.edu/fort.html > > Molecular modeling of organic and biological molecules; chemistry of lignin > and cellulose > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY)at(ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST)at(ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl)at(ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ From chemistry-request@ccl.net Thu Oct 30 03:50:00 2003 Received: from pasmtp.tele.dk (pasmtp.tele.dk [193.162.159.95]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9U8nTLj024033 for ; Thu, 30 Oct 2003 03:49:29 -0500 Received: from herodot (unknown [62.242.210.149]) by pasmtp.tele.dk (Postfix) with ESMTP id 2EDDC1EC365 for ; Thu, 30 Oct 2003 09:49:25 +0100 (CET) Received: from silex.dk (unknown [62.242.210.146]) by herodot (Postfix) with ESMTP id B915427D54 for ; Thu, 30 Oct 2003 09:49:11 +0100 (CET) Message-ID: <3FA0CEC5.8010502)at(silex.dk> Date: Thu, 30 Oct 2003 09:41:41 +0100 From: Kenneth Geisshirt Organization: Silex Science ApS User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031024 Debian/1.5-2 StumbleUpon/1.87 X-Accept-Language: da, en MIME-Version: 1.0 To: chemistry)at(ccl.net Subject: Re: CCL:Linux Cluster Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-0.1 required=7.0 tests=USER_AGENT_MOZILLA_UA,X_ACCEPT_LANG version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) ? Meana ? wrote: > We want to obtain information about building cluster of Linux. Where can we obtain it? First take a look at: http://www.beowulf.org http://www.tldp.org/HOWTO/Beowulf-HOWTO.html http://oscar.sourceforge.net A number of companies build clusters (e.g., the one I work for), and you can buy cluster distributions like MandrakeSoft's Clustering product. Finally, you can build a cluster by hand (ok if the number of nodes is less than 6). Kneth -- Kenneth Geisshirt - Principal Scientist Silex Science ApS, Trekronergade 126F, 4. sal, DK-2500 Valby, Denmark Phone: +45 4058 2178 - Fax: +45 3644 3539 - Web: www.silex.dk From chemistry-request@ccl.net Thu Oct 30 10:48:21 2003 Received: from kanssmtp05.aventis.com (kanssmtp05.aventis.com [198.80.25.22]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9UFlmLj012008 for ; Thu, 30 Oct 2003 10:47:49 -0500 Received: from kansmxsint01.pharma.aventis.com ([157.206.110.35]) by 204.126.89.34 with InterScan Messaging Security Suite; Thu, 30 Oct 2003 09:47:45 -0600 Received: from kansmxscon03.pharma.aventis.com ([157.206.110.83]) by kansmxsint01.pharma.aventis.com with Microsoft SMTPSVC(5.0.2195.6713); Thu, 30 Oct 2003 09:47:44 -0600 Received: from tucsmxsusr01.pharma.aventis.com ([155.65.124.47]) by kansmxscon03.pharma.aventis.com with Microsoft SMTPSVC(5.0.2195.6713); Thu, 30 Oct 2003 09:47:44 -0600 X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Subject: Virtual screening Date: Thu, 30 Oct 2003 08:47:43 -0700 Message-ID: <7E47908DD24B5243B1FEE5C4E29E7DA70977DC)at(tucsmxsusr01.pharma.aventis.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Virtual screening Thread-Index: AcOe/SfbLM42c8Y4Rd6eHJHNTB76yQ== From: To: X-OriginalArrivalTime: 30 Oct 2003 15:47:44.0309 (UTC) FILETIME=[28B0B650:01C39EFD] X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id h9UFmLLj012030 Dear All, I was wondering whether there is any studies/statistics regarding the success of virtual screening (including docking and pharmacophore based search) across different targets and/or target families. I have seen several publications that compare different docking softwares/scoring functions but I am not aware of any discussion regarding the success rate using pharmacophore search or docking approaches across various targets/target families. I really appreciate if someone could share their experiences or point me to the references. I will summarize the answers if there is interest for it. Thanks a lot. -Anil. anil.nair)at(aventis.com From chemistry-request@ccl.net Thu Oct 30 12:21:18 2003 Received: from webmail.mta.ca (postal.mta.ca [138.73.1.51]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9UHKlLj015161 for ; Thu, 30 Oct 2003 12:20:47 -0500 Received: from nobody by webmail.mta.ca with local (Exim 4.20) id 1AFGSL-0002Yp-0e for chemistry)at(ccl.net; Thu, 30 Oct 2003 13:19:33 -0400 Received: from 138.73.24.161 ( [138.73.24.161]) as user srwhttl)at(mailserv.mta.ca by webmail.mta.ca with HTTP; Thu, 30 Oct 2003 13:19:32 -0400 Message-ID: <1067534372.3fa14824f3402)at(webmail.mta.ca> Date: Thu, 30 Oct 2003 13:19:32 -0400 From: srwhttl)at(mta.ca To: chemistry)at(ccl.net Subject: Missing hydrogens: Viewing pdb crystal structures with Spartan and Gaussview03 MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit X-Originating-IP: 138.73.24.161 X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi everyone, I am having trouble trying to look at a crystal strucutre (from the Protein data bank). The veiwing programs I have tried (Spartan and Gaussview03) both ask me if I want "to add missing hydrogens", when I initally open the file. I click yes, but then it appears that the program has missed adding some hydrogens. This changes the multiplicity and charge, so it differs from the pdb file I want. Are there any suggestion to aovid this? If not, what are some other programs that have both viewing and building/editing capabilites (like spartan and Gaussiview) where I look at these crystal structures? Thanksing you in advance, Sarah Whittleton Mount Allison University Sackville, N.B., Canada From chemistry-request@ccl.net Thu Oct 30 17:09:25 2003 Received: from dswu83.btconnect.com (dswu83.btconnect.com [193.113.154.14]) by server.ccl.net (8.12.8/8.12.8) with SMTP id h9UM8rLj024711 for ; Thu, 30 Oct 2003 17:08:54 -0500 Received: from patriot (actually host 157.50.122.213.in-addr.arpa) by dswu83 with SMTP-CUST (XT-PP); Thu, 30 Oct 2003 22:11:34 +0000 From: "Roma Oakes" To: "ccl" Subject: RE: Symmetry and Gaussian Date: Thu, 30 Oct 2003 22:07:11 -0000 Message-ID: MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" 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 V6.00.2600.0000 Importance: Normal In-Reply-To: <5.1.1.6.0.20031029095508.00a1d9e0_at_mail.maine.edu> X-Spam-Status: No, hits=-1.4 required=7.0 tests=IN_REP_TO,MSGID_GOOD_EXCHANGE,QUOTED_EMAIL_TEXT version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Raymond I've come across this a few times myself - you need to use the iop 2/16=3. You simply add this to the route line so you might have: #p opt=tight rb3lyp/6-31g* iop(2/16=3) Iop 2/16 determines the action to be taken if the point group changes during an optimisation. option 0 = abort the job 1 = keep going 2 = keep going and leave symmetry on, using the old symmetry 3 = keep going and leave symmetry on, using the new symmetry Hope this helps Regards Roma > -----Original Message----- > From: Computational Chemistry List [mailto:chemistry-request_at_ccl.net]On > Behalf Of Raymond C. Fort Jr. > Sent: 29 October 2003 14:58 > To: chemistry_at_ccl.net > Subject: CCL:Symmetry and Gaussian > > > I'm sure this has been asked before, but the list archives currently are > not very searchable. I've been running some optimizations of small > molecules with G98 (ethylene, formaldehyde; Cartesian input) to > illustrate > use of the program to a class. The calculations fail rapidly with the > message that there has been a change in point group or standard > orientation. So far, the only way I can get a calculation to > finish is to > turn off symmetry. I'd appreciate suggestions of alternatives. > > Ray > > > Professor Ray Fort Jr. Voice: (207)-581-1180 > Department of Chemistry FAX: (207)-581-1191 > University of Maine EMail: rcfort_at_maine.edu > Orono, ME 04469 Web: > chemistry.umeche.maine.edu/fort.html > > Molecular modeling of organic and biological molecules; chemistry > of lignin > and cellulose > > > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your > Subject: line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: > CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl_at_ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > > From chemistry-request@ccl.net Thu Oct 30 16:42:26 2003 Received: from helix.nih.gov (helix.nih.gov [128.231.2.3]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9ULftLj023948 for ; Thu, 30 Oct 2003 16:41:55 -0500 Received: (from igorf@localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id h9ULfrK39078564; Thu, 30 Oct 2003 16:41:53 -0500 (EST) Date: Thu, 30 Oct 2003 16:41:52 -0500 From: Igor Filippov To: Kenneth Geisshirt cc: chemistry_at_ccl.net Subject: Re: CCL:Linux Cluster In-Reply-To: <3FA0CEC5.8010502_at_silex.dk> Message-ID: References: <3FA0CEC5.8010502_at_silex.dk> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.5 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) We have a hand-made cluster of 48 nodes. Why is the 6 node limit ??? Then there's biowulf - http://biowulf.nih.gov that has 500+ nodes, AFAIK at least a portion of it are not "made-ready" cluster boxes. As a side note, it's not clear what is it that Meana is asking about since IMHO the architecture of the cluster - hardware, network topology, software, configuration would seem to need to be determined from the proposed usage of the future cluster, and the original email neglected to mention anything about it. Sincerely, Igor Filippov Laborotory of Medicinal Chemistry NCI/SAIC-Frederick On Thu, 30 Oct 2003, Kenneth Geisshirt wrote: > ? Meana ? wrote: > > > We want to obtain information about building cluster of Linux. Where > can we obtain it? > > > First take a look at: > http://www.beowulf.org > http://www.tldp.org/HOWTO/Beowulf-HOWTO.html > http://oscar.sourceforge.net > > A number of companies build clusters (e.g., the one I work for), and you > can buy cluster distributions like MandrakeSoft's Clustering product. > Finally, you can build a cluster by hand (ok if the number of nodes is > less than 6). > > Kneth > -- > Kenneth Geisshirt - Principal Scientist > Silex Science ApS, Trekronergade 126F, 4. sal, DK-2500 Valby, Denmark > Phone: +45 4058 2178 - Fax: +45 3644 3539 - Web: www.silex.dk > > > > -= This is automatically added to each message by the mailing script =- > To send e-mail to subscribers of CCL put the string CCL: on your Subject: line > and send your message to: CHEMISTRY_at_ccl.net > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST_at_ccl.net > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > If your mail is bouncing from CCL.NET domain send it to the maintainer: > Jan Labanowski, jkl_at_ccl.net (read about it on CCL Home Page) > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > > > > From chemistry-request@ccl.net Thu Oct 30 22:04:33 2003 Received: from marcy.nas.nasa.gov (marcy.nas.nasa.gov [129.99.113.17]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9V342Lj015610 for ; Thu, 30 Oct 2003 22:04:02 -0500 Received: from localhost (ioana@localhost) by marcy.nas.nasa.gov (8.11.7p1+Sun/8.11.7/NAS-6n) with ESMTP id h9V341t15132 for ; Thu, 30 Oct 2003 19:04:02 -0800 (PST) Date: Thu, 30 Oct 2003 19:04:01 -0800 (PST) From: Ioana Cozmuta To: Computational Chemistry List Subject: SMD: constant velocity or force pulling? Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.0 tests=USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi CCL-ers, I would appreciate your advice related to the following matter: If you were extremely limited in the resources you have but you would have to run SMD simulations (SMD=steered MD) and you would have to chose between doing constant velocity pulling or constant force (acceleration) pulling, which one would you chose and based on which considerations? Thank you, Ioana From chemistry-request@ccl.net Thu Oct 30 18:08:35 2003 Received: from kafka.net.nih.gov (mailfwd.nih.gov [165.112.130.10]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id h9UN82Lj026871 for ; Thu, 30 Oct 2003 18:08:02 -0500 Received: from pollux.cber.nih.gov (pollux.cber.nih.gov [128.231.52.5]) by kafka.net.nih.gov (8.12.10/8.12.9) with ESMTP id h9UN82cD029412; Thu, 30 Oct 2003 18:08:02 -0500 (EST) Date: Thu, 30 Oct 2003 18:07:01 -0500 From: Rick Venable To: chemistry)at(ccl.net cc: Igor Filippov , Kenneth Geisshirt Subject: Re: CCL:Linux Cluster In-Reply-To: Message-ID: References: <3FA0CEC5.8010502)at(silex.dk> ReplyTo: Rick_Venable)at(nih.gov MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-1.1 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, RCVD_IN_NJABL,REFERENCES,REPLY_WITH_QUOTES,USER_AGENT_PINE, X_NJABL_OPEN_PROXY version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Another cluster setup option which I've used is the FAI package, with a homepage at URL http://www.informatik.uni-koeln.de/fai/ It is based on the Debian/GNU Linux distribution, which I was already using at my site. It's a more standardized, documented, and supported version of the sort of approach used to build "hand-made" clusters, by installing the OS and software packages in an automated way on a group of identical machines. I agree with Igor that you have to consider the applications, or at least their parallel potential and characteristics. Programs which require a lot of interprocess communication for parallel usage (such as most MD codes) may not scale very well when using ethernet to connect the hosts, esp. with the 2+ GHz speeds of current CPU chips. Several clusters here at NIH, including Biowulf, use Myrinet to connect cluster hosts, which gives greatly improved parallel scaling compared to ethernet. Myrinet is a bit expensive, but does work fairly well, via a modified MPICH library. As for job management, the PBS queueing system seems to be a fairly good option, and is available in 2 versions (one commercial, PBSpro). =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= Rick Venable 29/500 FDA/CBER/OVRR Biophysics Lab 1401 Rockville Pike HFM-419 Rockville, MD 20852-1448 U.S.A. (301) 496-1905 Rick_Venable)at(nih.gov ALT email: rvenable)at(speakeasy.org ------------------------------------- "Don't blame me, I voted for Kang." Homer =+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+=+= > > ? Meana ? wrote: > > > We want to obtain information about building cluster of Linux. > > > Where can we obtain it? > On Thu, 30 Oct 2003, Kenneth Geisshirt wrote: > > First take a look at: > > http://www.beowulf.org > > http://www.tldp.org/HOWTO/Beowulf-HOWTO.html > > http://oscar.sourceforge.net > > > > A number of companies build clusters (e.g., the one I work for), and > > you can buy cluster distributions like MandrakeSoft's Clustering > > product. Finally, you can build a cluster by hand (ok if the number > > of nodes is less than 6). On Thu, 30 Oct 2003, Igor Filippov wrote: > We have a hand-made cluster of 48 nodes. Why is the 6 node limit ??? > Then there's biowulf - http://biowulf.nih.gov that has 500+ nodes, > AFAIK at least a portion of it are not "made-ready" cluster boxes. > > As a side note, it's not clear what is it that Meana is asking about > since IMHO the architecture of the cluster - hardware, network > topology, software, configuration would seem to need to be determined > from the proposed usage of the future cluster, and the original email > neglected to mention anything about it.