From chemistry-request@ccl.net Thu Nov 6 04:38:18 2003 Received: from mail.it.helsinki.fi (mail.it.helsinki.fi [128.214.205.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA69baVc000473 for ; Thu, 6 Nov 2003 04:37:45 -0500 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by mail.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id hA69bMkP023824; Thu, 6 Nov 2003 11:37:22 +0200 (EET) Received: from soul.helsinki.fi (localhost [127.0.0.1]) by soul.helsinki.fi (8.12.10/8.12.10) with ESMTP id hA69bLDd341139; Thu, 6 Nov 2003 11:37:21 +0200 (EET) Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id hA69bLCO341149; Thu, 6 Nov 2003 11:37:21 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Thu, 6 Nov 2003 11:37:21 +0200 (EET) From: Mikael Johansson X-X-Sender: mpjohans^at^soul.helsinki.fi To: Steve Williams cc: CHEMISTRY^at^ccl.net Subject: Re: CCL:fractional nuclear charge In-Reply-To: <5.1.0.14.0.20031105122817.02717938^at^imap.appstate.edu> Message-ID: References: <5.1.0.14.0.20031105122817.02717938^at^imap.appstate.edu> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.4 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello Steve and All! On Wed, 5 Nov 2003, Steve Williams wrote: > I have a colleague who would like to some quantum chemistry calculations on > the following system: R-OH+ --> R-NH, that is, a smooth transition from an > open shell alcohol radical cation to a neutral radical amide. Is there a > way to do this? We discussed several options, based on what we have here: > 3) Is there existing code out there that already does this? With Turbomole (http://www.turbomole.com) you can do this. Or, I should say, you can at least define a fractional nuclear charge, and Turbomole performs the calculation. I tried HF, DFT and RI-MP2 on N2 with one of the N's having a q of +6.5. The basis set might be a problem, as they are optimised for specific atoms. I guess one way of getting around this would be to use a combined basis set for the metamorphosing atom, consisting of the BS of both the initial (O) and the final (N) atoms. Have a nice day, Mikael Johansson University of Helsinki Department of Chemistry mikael.johansson^at^helsinki.fi http://www.helsinki.fi/~mpjohans/ Phone: +358-9-191 50185 FAX : +358-9-191 50169 From chemistry-request@ccl.net Wed Nov 5 15:24:23 2003 Received: from smtpgw.sud-chemieinc.com ([208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5KNpVc012061 for ; Wed, 5 Nov 2003 15:23:52 -0500 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 75E9C47F9D; Wed, 5 Nov 2003 15:21:20 -0500 (EST) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 62E1147F90; Wed, 5 Nov 2003 15:21:20 -0500 (EST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.5329); Wed, 5 Nov 2003 15:23:50 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 Subject: RE: Bond order in gaussian Date: Wed, 5 Nov 2003 15:23:48 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0047FC39^at^srvkyem1.unitedcatalysts.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Bond order in gaussian Thread-Index: AcOjUhPm4ZN7wRGSTKeSMHfcWDfXwwAhnNoA From: "Shobe, David" To: Cc: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 05 Nov 2003 20:23:50.0016 (UTC) FILETIME=[B9198000:01C3A3DA] 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) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hA5KONVc012079 Ding, I think I figured this out: BD means a bonding orbital CR means a core orbital LP means a lone pair orbital RY* means a Rydberg orbital BD* means an antibonding orbital Important question: are there TWO of these tables? If so, one is for the alpha electrons and one is for the beta electrons. If the table you show is for the beta electrons only, the sum of 7 is correct. CCLers, am I right? --David Shobe -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request^at^ccl.net]On Behalf Of dxl^at^mail.ustc.edu.cn Sent: Tuesday, November 04, 2003 9:22 PM To: chemistry^at^ccl.net Subject: CCL:Bond order in gaussian Dear All I am try to do a bond order analysis with G98. Here is my test with O2 molecule. #B3LYP/6-31G opt pop=(NBO,Bonding) HF 0 3 O 0.00 0.00 0.000000 O 0.00 0.00 1.200000 The last lines of the output file is below, and I don't think it is right. How can I read the table correctly? And what the LP,RY* stand for? Thank you very much for your help!!!!!!!!!!!!!!!!! Natural Bond Orbitals (Summary): Principal Delocalizations NBO Occupancy Energy (geminal,vicinal,remote) =============================================================================== Molecular unit 1 (O2) 1. BD ( 1) O 1- O 2 1.00000 -1.03224 2. BD ( 2) O 1- O 2 1.00000 -0.45369 3. BD ( 3) O 1- O 2 1.00000 -0.45369 4. CR ( 1) O 1 0.99997 -19.14436 12(v) 5. CR ( 1) O 2 0.99997 -19.14436 8(v) 6. LP ( 1) O 1 0.99984 -0.87950 12(v) 7. LP ( 1) O 2 0.99984 -0.87950 8(v) 8. RY*( 1) O 1 0.00019 0.95747 9. RY*( 2) O 1 0.00000 0.88719 10. RY*( 3) O 1 0.00000 0.88719 11. RY*( 4) O 1 0.00000 1.07773 12. RY*( 1) O 2 0.00019 0.95747 13. RY*( 2) O 2 0.00000 0.88719 14. RY*( 3) O 2 0.00000 0.88719 15. RY*( 4) O 2 0.00000 1.07773 16. BD*( 1) O 1- O 2 0.00000 0.26370 17. BD*( 2) O 1- O 2 0.00000 -0.13403 18. BD*( 3) O 1- O 2 0.00000 -0.13403 ------------------------------- Total Lewis 6.99962 ( 99.9946) Valence non-Lewis 0.00000 ( 0.0000) Rydberg non-Lewis 0.00038 ( 0.0054) ------------------------------- Total unit 1 7.00000 (100.0000) Charge unit 1 1.00000 Ding Xunlei 2003-11-05 ______________________________________________ Ding Xunlei, Ph.D. Candidate Open Laboratory of Bond Selective Chemistry University of Science & Technology of China Hefei, Anhui 230026, P.R.China Tel.: 0086-551-3603418 Fax.: 0086-551-3602969 E-mail: dxl^at^mail.ustc.edu.cn Http://www.bsc.ustc.edu.cn/~dxl = = = = = = = = = = = = = = = = = = = = -= 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 Wed Nov 5 23:24:28 2003 Received: from forthnet.gr (athmta03.forthnet.gr [193.92.150.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA64NXVc024364 for ; Wed, 5 Nov 2003 23:23:44 -0500 Received: from wseas.org (ppp1-adsl-21.ath.forthnet.gr [213.16.180.21]) by forthnet.gr (8.12.2-20030919/8.12.2) with SMTP id hA64NWg7006329 for ; Thu, 6 Nov 2003 06:23:33 +0200 Message-Id: <200311060423.hA64NWg7006329^at^forthnet.gr> From: "Katerina Tsironi" To: Subject: 4th WSEAS International Conference on MATHEMATICS AND COMPUTERS IN BIOLOGY AND CHEMISTRY (MCBC'03) with special emphasis on: BIOENGINEERING, MOLECULAR BIOLOGY, MATHEMATICAL BIOLOGY, BIOCHEMISTRY, BIOPHYSICS, COMPUTER BIOLOGY, BIOLOGICAL DYNAMICAL SYSTEMS, Sender: "Katerina Tsironi" Mime-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Nov 2003 06:23:25 +0200 Content-Transfer-Encoding: 8bit X-Spam-Status: No, hits=1.1 required=7.0 tests=MSG_ID_ADDED_BY_MTA_3,UPPERCASE_50_75 version=2.55 X-Spam-Level: * X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) WSEAS will reply to you only if you write the word: WSEAS somewhere in the Subject of your message, In case that you forgot it, unfortunately, there is not any automatic reply or warning! ----------------------------------------------------------------------------------- EXTENDED DEADLINE: Nov.15, 2003 FORWARD THIS EMAIL TO YOUR MAILING LISTS PLEASE! 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From chemistry-request@ccl.net Wed Nov 5 20:24:01 2003 Received: from mail2.qmul.ac.uk (mail2.qmul.ac.uk [138.37.6.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA61NTVc019005 for ; Wed, 5 Nov 2003 20:23:30 -0500 Received: from smtp.qmul.ac.uk ([138.37.6.40]) by mail2.qmul.ac.uk with esmtp (Exim 4.14) id 1AHYrw-0001aw-MA for CHEMISTRY)at(ccl.net; Thu, 06 Nov 2003 01:23:28 +0000 Received: from [138.37.41.26] (helo=ruzhen) by smtp.qmul.ac.uk with esmtp (Exim 3.35 #5) id 1AHYrv-0006hY-00 for CHEMISTRY)at(ccl.net; Thu, 06 Nov 2003 01:23:27 +0000 Date: Thu, 6 Nov 2003 1:22:5 +0000 From: "Ru-Zhen,Li" To: "CHEMISTRY)at(ccl.net" Subject: build amyloid peptide by hand--problem in peptide bond!!! Organization: Materials Department, Queen Mary, University of London X-mailer: Foxmail 4.1 [eg] Mime-Version: 1.0 Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: 7bit Message-Id: X-Sender-Host-Address: 138.37.41.26 X-QM-Scan-VirusCheck: clean X-Spam-Status: No, hits=2.3 required=7.0 tests=INVALID_DATE,PLING_PLING version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Dear all, I was trying to build a amyloid peptide with the builder module in Insight2, the sequence is DAEFR---HDSGY---EVHHQ---KLVFF---AEDVG---SNKGA---IIGLM---VGGVV---IAT What I am confused is: as we all know, there are two hydrogens on the amino group, and if I choose different hydrogen to form the peptide bond with the carboxylic acid group from the previous amino acids, I will have different structure, one is quite global, and another is quite linear. what I really what to know is, since the amino acids is not symmetrical, the two hydrogens must be different to construct the secondary structure, shall I just select the two hydrogens randomly or shall I select a particular hydrogen? the peptide might choose the structure which has the lowest energy, but the problem is, since there are so many amino acids, there will be too many possibilities, how can I know which one is right? can anyone tell me what is the truth in real protein? does any one have similiar experience before? i mean build a peptide chain by hand? thank you very much in deed!! best regards Ru-Zhen Best regards. Ru-Zhen,Li r.li)at(qmul.ac.uk 2003-11-06 From chemistry-request@ccl.net Wed Nov 5 21:36:04 2003 Received: from rama.ks.uiuc.edu (rama.ks.uiuc.edu [130.126.120.150]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA62ZWVc021161 for ; Wed, 5 Nov 2003 21:35:32 -0500 Received: from santiago.ks.uiuc.edu (santiago.ks.uiuc.edu [130.126.120.99]) by rama.ks.uiuc.edu (8.12.10/8.12.10) with ESMTP id hA62ZWu5004297; Wed, 5 Nov 2003 20:35:32 -0600 (CST) Received: from localhost (jim@localhost) by santiago.ks.uiuc.edu (8.11.6/8.9.3) with ESMTP id hA62ZWN08226; Wed, 5 Nov 2003 20:35:32 -0600 X-Authentication-Warning: santiago.ks.uiuc.edu: jim owned process doing -bs Date: Wed, 5 Nov 2003 20:35:32 -0600 (CST) From: Jim Phillips To: Robert Duke cc: chemistry{at}ccl.net Subject: Re: CCL:PMEMD 3.1 Release - High Scalability Update to PMEMD In-Reply-To: <009901c3a24d$193f0d90$88541a42@bobcat> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.4 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi again, On Mon, 3 Nov 2003, Robert Duke wrote: > reciprocal force computation. I would like to see a 92K atom benchmark with > 8 A cutoffs in which you all get 10 nsec/day on 1024 processors at EPCC Me too. Stay tuned (but no promises). > (;-}). I presumed you all were actually using the larger cutoff to > compensate for errors associated with the use of a multi-timestep approach The main limitation on impulse-based multiple timestepping is a non-linear resonance at half the highest frequency normal mode of the molecule, or about 5 fs. This can be higher if you constrain bonds to hydrogens. If you're really picky about energy conservation there are other resonances, but the energy drift is very slight. One can also use very light Langevin damping to erase these effects. > for PME, or simply because using a larger timestep would make the simulation > scale better, though perhaps have worse low-end performance. I have never The apoa1 benchmark started as a cutoff benchmark and had PME added later. If there is a consensus among the CHARMM and AMBER communities that 8A is sufficient with PME, then NAMD users can run with 8A. The effect of cutoff on NAMD scaling is that there is more work, but there are also fewer spatial domains to distribute. For example, apoa1 with 12A cutoff has only 6x6x4=144 domains, while your FIX (thanks!) at 8A has 11x7x6=462 domains. These cancel each other out somewhat. > seen it to be necessary to use such a large cutoff, and indeed pmemd and > sander 6/7 would have more trouble with really large cutoffs because they > use pairlists. We used a 1.5 fs step for both the PME and direct force NAMD 2.5 uses pairlists, but only 256MB of memory for a 92K atom system with a 12A cutoff, and the pairlist data is distributed in parallel runs. You can also turn pairlists off if you're short on memory. > parts of the calculation, which gives us good results, even with highly > ionic systems (the FIX benchmark is for a protein with > gamma-carboxyglutamates and Ca++'s all over the place; the system is from > published work). It is a nice benchmark (thanks again). I hope you can make it public. > Well, lets do apples and apples on your favorite machine, lemieux, which > NAMD has been optimized for, and which PMEMD has NOT been optimized for > (stock mpi; no fancy attempts to structure the code to the machine > architecture or compiler; in fact I do not know the machine well at all and > have limited access). Over the weekend I ran a series of benchmarks on > lemieux on the JAC benchmark which you referenced below. I deviated from > the exact benchmark specification in two inconsequential ways: 1) I did 4000 > step simulations to get more accurate times, and 2) I used a "skinnb" of 1.0 > instead of 2.0. PMEMD and Sander 6/7 by default check for atom movement > exceeding the skin, so the skinnb parameter is an optimization parameter, > and PMEMD does better with it set to 1.0 (ie., this in no way affects > results of the simulation, PMEMD just builds smaller lists more frequently). I've just done the same with the NAMD 2.5 released binary. NAMD 2.5 dynamically adjusts pairlistdist (and temporarily and locally disables pairlists in the case of a violation), so I started it at 10A (9A cutoff). This is the time on Lemeiux from the last 1000 steps of a 4000 step run, using the direct Elan implementation of Charm++ and the "+strategy USE_MESH" command line option: nodes procs time (s) 1 4 222.122 2 8 115.277 4 16 59.4164 8 32 34.3925 16 64 22.2451 32 128 12.8739 64 256 9.90325 I'll leave your data below for comparison. The first surprise is that for such different programs (FORTRAN 90 vs C++) the 4 processor times are shockingly similar, and the race is tied up to 64 processors. However, NAMD continues scaling up to 128 processors, at which point we hit the frustrating 10ms/step barrier. I've skipped the academic exercise of running fewer processors per node, and this isn't the right forum to discuss the fundamental limits of the machine (SC 2003 in two weeks is). For NAMD the 50% mark is at about 128 CPUs. > JAC Benchmark, 23558 atoms on lemieux.psc.edu, results in wall clock seconds > per 1000 steps. > > #cpu #nodes PMEMD 3.1 wc sec NAMD 2.4 wc sec PMEMD/NAMD speedup > > 1 1 828.5 1385 1.67x > 2 1 431.5 750 1.74x > 4 1 218.25 390 1.79x > 8 2 118.5 198 1.67x > 16 4 67.25 105 1.56x > 32 8 37 61 1.65x > 64 16 22.25 40 1.80x > 72 24 19 nd nd > 96 32 17.75 nd nd > 120 40 18.75 nd nd > 128 32 22 23 1.05 In any case, competition is healthy and PMEMD is certainly a worthy and welcome competitor for NAMD. Stay tuned to CCL for NAMD FIX benchmark results on the HPCx (EPCC) SP. -Jim From chemistry-request@ccl.net Wed Nov 5 15:39:02 2003 Received: from smtpgw.sud-chemieinc.com ([208.23.162.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA5KcVVc012379 for ; Wed, 5 Nov 2003 15:38:31 -0500 Received: from smtpgw.sud-chemieinc.com (smtpgw.sud-chemieinc.com [127.0.0.1]) by localhost.sud-chemieinc.com (Postfix) with ESMTP id 5632E47FA4; Wed, 5 Nov 2003 15:36:01 -0500 (EST) Received: from srvkyec1.americas.sc-world.com (srvkyec1.americas.sc-world.com [10.16.100.11]) by smtpgw.sud-chemieinc.com (Postfix) with ESMTP id 4110E47FA0; Wed, 5 Nov 2003 15:36:01 -0500 (EST) Received: from srvkyem1.americas.sc-world.com ([10.16.100.68]) by srvkyec1.americas.sc-world.com with Microsoft SMTPSVC(5.0.2195.5329); Wed, 5 Nov 2003 15:38:30 -0500 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-MimeOLE: Produced By Microsoft Exchange V6.0.6487.1 Subject: RE: fractional nuclear charge Date: Wed, 5 Nov 2003 15:38:29 -0500 Message-ID: <9DD56492790889439F731F5BD6DACA0047FC3A{at}srvkyem1.unitedcatalysts.com> X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: fractional nuclear charge Thread-Index: AcOjzLp2uiIOfSWlQ1uj9+bX64quZAADqKgA From: "Shobe, David" To: "Steve Williams" Cc: "CCL computational chemistry list (E-mail)" X-OriginalArrivalTime: 05 Nov 2003 20:38:30.0923 (UTC) FILETIME=[C6293DB0:01C3A3DC] 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) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hA5Kd2Vc012390 Steve, I don't think this is possible with Gaussian, but I remember trying a noninteger nuclear charge in GAMESS(US), and I think it was accepted by the program. Good luck finding basis sets for Z = 7.5! ;-) --David Shobe, Ph.D., M.L.S. S|d-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- From: Computational Chemistry List [mailto:chemistry-request{at}ccl.net]On Behalf Of Steve Williams Sent: Wednesday, November 05, 2003 12:41 PM To: CHEMISTRY{at}ccl.net Subject: CCL:fractional nuclear charge I have a colleague who would like to some quantum chemistry calculations on the following system: R-OH+ --> R-NH, that is, a smooth transition from an open shell alcohol radical cation to a neutral radical amide. Is there a way to do this? We discussed several options, based on what we have here: 1) Is there and IOP in G98 that would allow a particular nucleus to have a fractional charge so that a series of calculations he could gradually go > from Z=7 to Z=8? 2) If not, how hard would this be to do with a program where we can play with the source code, like GAMESS or perhaps NWCHEM? 3) Is there existing code out there that already does this? Thanks, Steve Steve Williams A. R. Smith Department of Chemistry Appalachian State University Boone, NC 28608 USA 828-262-2965 -= 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 Wed Nov 5 21:02:10 2003 Received: from mx1.ustc.edu.cn ([218.22.21.1]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA621aVc020035 for ; Wed, 5 Nov 2003 21:01:38 -0500 Received: from dxl ([202.38.82.79]) by mx1.ustc.edu.cn (8.8.7/8.8.6) with ESMTP id JAA23966; Thu, 6 Nov 2003 09:56:37 +0800 Message-Id: <200311060156.JAA23966.-at-.mx1.ustc.edu.cn> Date: Thu, 6 Nov 2003 9:58:5 +0800 From: 6!Q8@W Reply-To: dxl.-at-.mail.ustc.edu.cn To: CCL , gausshelp Subject: Re: CCL:Bond order in gaussian-a GOOD result! Organization: VP9z?F4sQ!<|;/Q'J5QiJR X-mailer: FoxMail 4.0 beta 2 [cn] Mime-Version: 1.0 Content-Type: multipart/mixed; boundary="=====000_Dragon824224344442_=====" X-Spam-Status: No, hits=5.6 required=7.0 tests=BASE64_ENC_TEXT,DATE_IN_PAST_06_12,HEADER_8BITS, INVALID_DATE,RCVD_IN_RFCI version=2.55 X-Spam-Level: ***** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. --=====000_Dragon824224344442_===== Content-Type: text/plain; charset="GB2312" Content-Transfer-Encoding: base64 RGVhciBDQ0yjug0KDQqhoaGhSSBoYXZlIG1hZGUgYSBtaXN0YWtlIHRoYXQgTzIgbW9sZWN1bGUg J3MgYm9uZCBvcmRlciBpcyAyLg0KCQkNCglJbiB0aGUgY2FsY3VsYXRpb24gd2l0aCBPMiBtb2xl Y3VsZSB3aXRoICNCM0xZUC82LTMxRyBvcHQgcG9wPU5CTywNCglJIGdldCBPTkUgYWxmYSBlbGVj dHJvbiBpbiAgIEJELCBhbmQgVEhSRUUgYmV0YSBlbGVjdHJvbnMgaW4gQkQuDQoJQW5kIHRoZXJl IGlzIG5vIGVsZWN0cm9ucyBpbiAgQkQqLiBUaG91Z2ggdGhpcyBpcyBub3QgdGhlIHJpZ2h0DQoJ ZWxlY3Ryb25pYyBjb25maWd1cmF0aW9uLCBpdCBnaXZlcyB0aGUgY29ycmVjdCBib25kIG9yZGVy IGFzIDIuDQoJDQoJQ2FuIEkgdXNlIHRoZSBtZXRob2QgdG8gZG8gb3RoZXJzIGpvYiA/IA0KDQoJ RWxld2FycyBhbmQgV2lsbGlhbSB0b2xkIG1lIHRvIHVzZSBQb3AobmJvcmVhZCksIHRoYW5rIHlv dSENCg0KCUkgdHJ5IHRoaXMgY2FsY3VsYXRpb24gd2l0aCAjQjNMWVAvNi0zMTErRygzZGYpIG9w dCBQb3AobmJvcmVhZCkNCglhbmQgdGhlIFdpYmVyZyBib25kIGluZGV4IGlzIGJlbG93Og0KCQ0K CVRvdGFsOjEuNTE4NQ0KCWFsZmEgOjAuMjYyMCAgICh3aXRoIGFyb3VuZCAxIGVsZWN0cm9uICBp biBCRCBhbmQgMCBlbGVjdHJvbiBpbiBCRCopDQoJYmV0YSA6MC43NTIxICAgKHdpdGggYXJvdW5k IDMgZWxlY3Ryb25zIGluIEJEIGFuZCAwIGVsZWN0cm9uIGluIEJEKikNCg0KCUkgdGhpbmsgd2Ug Y2FuIGdldCB0aGUgcmlnaHQgYm9uZCBvcmRlciBhcyAoMC4yNjIwKzAuNzUyMSkqMj0yLjAyODIu DQoJVGhlIHRvdGFsIGdpdmVzIHRoZSB3cm9uZyB2YWx1ZS4NCgkNCglUaGlzIG1ldGhvZCBpcyBj b25maXJtZWQgYnkgdGhlIGNhbGN1bGF0aW9uIHdpdGggc2luZ2xldCBPMiBtb2xlY3VsZSwNCgl3 aXRoICAjdUIzTFlQLzYtMzExK0coM2RmKSBvcHQgUG9wKE5PQUIsbmJvcmVhZCkNCgkNCglUb3Rh bDogMi4wMzI0DQoJYWxmYSA6IDAuNTA4MQ0KCWFsZmEgOiAwLjUwODENCgkNCgl0aGUgcmlnaHQg Ym9uZCBvcmRlciBhcyAoMC41MDgxKzAuNTA4MSkqMj0yLjAyODIuDQoJVGhlIHRvdGFsIGdpdmVz IGFsc28gdGhlIHJpZ2h0IHZhbHVlLCBJIHRoaW5rICwgZm9yIHRoaXMgaXMgYSBzaW5nbGV0IA0K CWNhbGN1bGF0aW9uLg0KCQ0KCUFNIEkgUklHSFQ/DQoJDQogICAgVGhhbmsgeW91IGZvciB5b3Vy IGhlbHAhoaGhoaGhoaGhoaGhoaGhoQ0KIAkJCQkNCqGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGh oaFEaW5nIFh1bmxlaQ0KoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoaGhoTIwMDMtMTEtMDYNCl9f X19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX19fX18NCkRpbmcgWHVubGVp LCBQaC5ELiBDYW5kaWRhdGUNCk9wZW4gTGFib3JhdG9yeSBvZiBCb25kIFNlbGVjdGl2ZSBDaGVt aXN0cnkNClVuaXZlcnNpdHkgb2YgU2NpZW5jZSAmIFRlY2hub2xvZ3kgb2YgQ2hpbmENCkhlZmVp LCBBbmh1aSAyMzAwMjYsIFAuUi5DaGluYQ0KVGVsLjogMDA4Ni01NTEtMzYwMzQxOA0KRmF4Ljog MDA4Ni01NTEtMzYwMjk2OQ0KRS1tYWlsOiBkeGxAbWFpbC51c3RjLmVkdS5jbg0KSHR0cDovL3d3 dy5ic2MudXN0Yy5lZHUuY24vfmR4bA0K --=====000_Dragon824224344442_===== Content-Type: image/gif; name="LittleBoy.GIF" Content-Transfer-Encoding: base64 Content-Disposition: FoxmailIcon; filename="LittleBoy.GIF" R0lGODlhIAAgANQAAGCXzwCAgGBnYP/IkPzJmpFjPBsNA2Q8HxQDACIGAk4HADYDAA0AAP///wAA ANPT05KSkm5ubmVlZUZGRiUlJRgYGBEREQ8PDwcHBwMDAwAAAAAAAAAAAAAAAAAAAAAAACH/C05F VFNDQVBFMi4wAwEAAAAh/sJodHRwOi8vd3d3LnJ0bHNvZnQuY29tL2FuaW1hZ2ljLwoKQ3JlYXRl ZCB3aXRoIEFuaW1hZ2ljIEdJRiBWIDEuMjJhCmJ5IFJpZ2h0IHRvIExlZnQgU29mdHdhcmUgSW5j LgoKVG8gc3VwcHJlc3MgdGhpcyBtZXNzYWdlIGluIHRoZSByZWdpc3RlcmVkIHZlcnNpb24KdW5j aGVjayAiT3B0aW9ucyB8IEFuaW1hZ2ljIGNvbW1lbnQgZnJhbWUiCgAh+QQJGQABACwAAAAAIAAg AAAF1mAgjmRpnmiqrqrjvjCLugNsO3LpDPz91rgcggf07XqyYa/nI9ZWytqy6HQGT1HrtEq8mhjc 45b7NImB5DTSrP6py6UoLfweLEwGpuBcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41AApdqkiIO CUxdjJppnAGBYYyQBQUERAoleW2QRAWuJFmOfbW1rySnfVy7A70jsV3ARAc8xCO/RXNkC8rDWGGz ZAgpzsgD2Srbfd4rCZ/ALjki5OXWXjKWoz2D6AEvooM2ojEtAADvqfz+BgE0EQIAIfkECRkAAQAs AAAAACAAIAAABc5gII5kaZ5oqq6q474wi7oDbDty6Qz8/da4HIIH9O16smGv5yPWVsrasuh0Bk9R 67RKvJoY3OOW+zSJgeQ00qz+qculKC38HixMhum5TryXwFKBVHV+JA55R2KJhGZgMFt7XIUjDglM XZhvkyKAYW5OBQUERAoleW2RRAWkJFldqVWrq6UknXxcsgO0I6eZtwMHPLsjtkVzZAvBulievwgp xb8DzyrRfNQrCZa3Ljki2tueXjIODeaR5eMrL+bnNu0xLQAA5e0NDvP18PkmIQAh+QQJGQABACwA AAAAIAAgAAAF02AgjmRpnmiqrqrjvjCLug9sO3LpPPz91rgchgf07XqyYa/nI9ZWytqy6HQGT1Hr tEq8mjLc45b7NImB5DTSrP6py6UoLfx+VEwWpuRcJ95LYEANYm5vfyQOeQ4Ng12LfFyHIw5gi41A EpdqkiIOF0xdjJppnAGBYYyQERFOFCV5bZBErDyuI1mOfaystiOnfVy7D70isF3ARBO1X1U2m8rD WGGyZBgpv8g81irYwNsrF5/ALjki4eLTXjKWoz2D5QEvooM2ojEtEBDsqfn7g/0mQgAAOw== --=====000_Dragon824224344442_=====-- From chemistry-request@ccl.net Wed Nov 5 19:32:34 2003 Received: from etsuex1.etsu.edu (etsuex1.etsu.edu [151.141.8.103]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA60W3Vc017312 for ; Wed, 5 Nov 2003 19:32:03 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6375.0 content-class: urn:content-classes:message MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----_=_NextPart_001_01C3A3FD.65A9DF44" Subject: Dual Xeon G98 Summary Date: Wed, 5 Nov 2003 19:32:02 -0500 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: Dual Xeon G98 Summary Thread-Index: AcOj/Wa4i5R5Fg5pEdiPpgBAlXb8og== From: "Close, David M." To: X-Spam-Status: No, hits=0.2 required=7.0 tests=HTML_60_70,HTML_MESSAGE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------_=_NextPart_001_01C3A3FD.65A9DF44 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable CCL'ers: Thanks so much for the quick replies. I have the system working = now. Some who wrote me asked questions like, Was I logged in as root?, and = did I have the SMP Kernel loaded? Also some thought that LINDA was needed to run 2 processors on a = "parallel" job. This is not the case however. The answer was simply to balance the "bytes" read into shmmax with the = %mem=3D line in the input file. So for my 512 Mb total memory and 2 processors, the suggestion was to = put 2/3 of available memory as shared memory. So 340 Mb is 356515840 = bytes. =20 This is done with echo "356515840" >/proc/sys/kernel/shmmax. =20 I ran a test job of an OPT on the N1-H deprotonated cytosine cation = with B3LYP/6-31+G(d) which took 3 hours and 18 minutes with a single = processor and 1 hour 51 minutes with %Nproc=3D2. That's 1.78 times = faster. =20 I thank everyone who help out with this. Regards, Dave Close. =20 ------_=_NextPart_001_01C3A3FD.65A9DF44 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable

=A0 = CCL’ers:

=A0=A0=A0 = Thanks so much for the quick replies.=A0 I have the = system working now.

=A0 Some who = wrote me asked questions like, Was I logged in as root?, and did I have the SMP Kernel = loaded?

=A0 Also some = thought that LINDA was needed to run 2 processors on a “parallel” = job.=A0 This is not the case = however.

=A0 The = answer was simply to balance the “bytes” read into shmmax with the = %mem=3D line in the input file.

=A0 So for my = 512 Mb total memory and 2 processors, the suggestion was to put 2/3 of = available memory as shared memory.=A0 So = 340 Mb is 356515840 bytes.

 

=A0 This is = done with echo “356515840” = >/proc/sys/kernel/shmmax.

 

=A0 I ran a = test job of an OPT on the N1-H deprotonated cytosine cation with B3LYP/6-31+G(d) = which took 3 hours and 18 minutes with a single processor and 1 hour 51 minutes = with %Nproc=3D2. That’s 1.78 times faster.

 

=A0 I thank = everyone who help out with this.

=A0 Regards, = Dave Close.

 

=00 ------_=_NextPart_001_01C3A3FD.65A9DF44-- From chemistry-request@ccl.net Thu Nov 6 10:31:09 2003 Received: from sungoddess.ccs.yorku.ca (sungoddess.ccs.yorku.ca [130.63.236.144]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6FUbVc011007 for ; Thu, 6 Nov 2003 10:30:37 -0500 Received: from mountain.chem.yorku.ca (mountain.chem.yorku.ca [130.63.133.28]) by sungoddess.ccs.yorku.ca (8.12.10/8.12.8) with SMTP id hA6FUWcq000984; Thu, 6 Nov 2003 10:30:36 -0500 (EST) Date: Thu, 6 Nov 2003 10:17:03 -0500 (EST) From: Rene Fournier - 1999-07-07 X-Sender: renef!at!mountain.chem.yorku.ca To: Mikael Johansson cc: Steve Williams , CHEMISTRY!at!ccl.net Subject: Re: CCL:fractional nuclear charge In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-0.5 required=7.0 tests=IN_REP_TO,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello Steve, Mikael, Everyone: As Mikael wrote, with fractional nuclear charges... >The basis set might be a problem, as they are optimised for specific >atoms. I totally agree. >I guess one way of getting around this would be to use a combined >basis set for the metamorphosing atom, consisting of the BS of both >the initial (O) and the final (N) atoms. I am afraid this might give problems with near linear dependencies, maybe inacurrate inversion of the overlap matrix. A way around that problem would be to define an "intermediate basis set" by interpolating two (preferably large) O and N basis sets that have the same contraction pattern, ie, a "metamorphosing basis set for a metamorphosing atom". I have a related question: does anyone know of a program that would allow to use positive charge distributions other than a set of point charges, for instance, a set of spherical Gaussian distributions. -- Rene ------------------------------------------ | Rene Fournier, Associate Professor | | Chemistry Dpt, York University | | 4700 Keele Street, Toronto | | Ontario, CANADA M3J 1P3 | ------------------------------------------ From chemistry-request@ccl.net Thu Nov 6 10:19:08 2003 Received: from brown.csi.cam.ac.uk (brown.csi.cam.ac.uk [131.111.8.14]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6FIbVc010680 for ; Thu, 6 Nov 2003 10:18:37 -0500 Received: from ucctemp2.ch.cam.ac.uk ([131.111.121.37] helo=uni-koeln.de) by brown.csi.cam.ac.uk with esmtp (Exim 4.20) id 1AHltn-0004AJ-7F for chemistry.-at-.ccl.net; Thu, 06 Nov 2003 15:18:15 +0000 Message-ID: <3FAA663B.6070907.-at-.uni-koeln.de> Date: Thu, 06 Nov 2003 16:18:19 +0100 From: Christoph Steinbeck Reply-To: c.steinbeck.-at-.uni-koeln.de User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.5) Gecko/20031013 Thunderbird/0.3 X-Accept-Language: en-us, en MIME-Version: 1.0 To: "CCL computational chemistry list (E-mail)" Subject: NMRShiftDB: An Open Access, Open Submission NMR database Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Cam-ScannerInfo: http://www.cam.ac.uk/cs/email/scanner/ X-Cam-AntiVirus: No virus found X-Cam-SpamDetails: Not scanned 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) We are pleased to announce the release of version 1.0 of our open access, open submission, open source NMR database NMRShiftDB. The database lives on http://www.nmrshiftdb.org and can be accessed via a web interface. The software and database content can be downloaded via http://www.sourceforge.net/projects/nmrshiftdb. NMRShiftDB allows for searching for (sub-)spectra, (sub-)structures and other properties (chemical names, measurement conditions, keywords), and last not least 13C spectrum prediction based on the database content. Currently, the database contains about 5300 structures and about 6000 assigned spectra. We very much welcome contributions of datasets or any other type of collaboration. Please note that due to our open content model, there is no danger of seeing your datasets vanish behind any virtual or real walls. The current and future content of NMRShiftDB is and will always be downloadable via the above URL together with the software to make them searchable. Thus, anyone is capable (and cordially invited) to create his or her own NMRShiftDB mirror. Feel free to contact the author of this mail, if you are interested. A technical paper on the database has just appeared in J. Chem. Inf. Comput. Sci, ASAP section, http://dx.doi.org/10.1021/ci0341363 Cheers, Christoph Steinbeck -- Dr. Christoph Steinbeck (e-mail: c.steinbeck.-at-.uni-koeln.de) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z|lpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. From chemistry-request@ccl.net Thu Nov 6 10:14:46 2003 Received: from mailserv.unb.ca (mailserv.unb.ca [131.202.3.23]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6FEEVc010557 for ; Thu, 6 Nov 2003 10:14:14 -0500 Received: from gollum.unb.ca (gollum.unb.ca [131.202.3.51]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id hA6FEDdP011044 for ; Thu, 6 Nov 2003 11:14:13 -0400 Received: from gollum.unb.ca (localhost.localdomain [127.0.0.1]) by gollum.unb.ca (8.12.8/8.12.8) with ESMTP id hA6FEDjS019143 for ; Thu, 6 Nov 2003 11:14:13 -0400 Received: (from apache@localhost) by gollum.unb.ca (8.12.8/8.12.8/Submit) id hA6FECd1019138 for chemistry.-at-.ccl.net; Thu, 6 Nov 2003 11:14:12 -0400 Received: from athlon2.chem.unb.ca (athlon2.chem.unb.ca [131.202.171.176]) by webmail.unb.ca (IMP) with HTTP for ; Thu, 6 Nov 2003 11:14:12 -0400 Message-ID: <1068131652.3faa6544c4f16.-at-.webmail.unb.ca> Date: Thu, 6 Nov 2003 11:14:12 -0400 From: Joey Harriman To: CCL posting Subject: clustering database molecules MIME-Version: 1.0 Content-Type: text/plain; charset=ISO-8859-1 Content-Transfer-Encoding: 8bit User-Agent: Internet Messaging Program (IMP) 3.2.2 X-Originating-IP: 131.202.171.176 X-MailScanner-Information: Please contact the ISP for more information X-UNB-VirusScanner: Found to be clean X-UNB-SpamDetails: not spam (whitelisted), SpamAssassin (score=-0.6, required 5, SPAM_PHRASE_02_03, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-0.3 required=7.0 tests=USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi, I am trying to cluster a database of a tetrapeptide with different geometries. I am currently using MOE and have tried varying fingerprints (at the 99%) threshold with no success. Does anyone have a good system for clustering different geometries of the same molecule from a database? Thanks in advance for any help you can offer. Joey ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o.-at-.unb.ca 476-6543 ---------------------------------- From chemistry-request@ccl.net Thu Nov 6 11:53:56 2003 Received: from mail.it.helsinki.fi (mail.it.helsinki.fi [128.214.205.39]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6GrOVc013316 for ; Thu, 6 Nov 2003 11:53:24 -0500 Received: from soul.helsinki.fi (soul.helsinki.fi [128.214.3.1]) by mail.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id hA6GqhkP005746; Thu, 6 Nov 2003 18:52:43 +0200 (EET) Received: from soul.helsinki.fi (localhost [127.0.0.1]) by soul.helsinki.fi (8.12.10/8.12.10) with ESMTP id hA6GqhDd343230; Thu, 6 Nov 2003 18:52:43 +0200 (EET) Received: from localhost (mpjohans@localhost) by soul.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id hA6Gqha2343181; Thu, 6 Nov 2003 18:52:43 +0200 (EET) X-Authentication-Warning: soul.helsinki.fi: mpjohans owned process doing -bs Date: Thu, 6 Nov 2003 18:52:43 +0200 (EET) From: Mikael Johansson X-X-Sender: mpjohans^at^soul.helsinki.fi To: Rene Fournier - 1999-07-07 cc: Steve Williams , CHEMISTRY^at^ccl.net Subject: Re: CCL:fractional nuclear charge In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.9 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,USER_AGENT_PINE,X_AUTH_WARNING version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hello Rene, Steve, and All! On Thu, 6 Nov 2003, Rene Fournier - 1999-07-07 wrote: > I am afraid this might give problems with near linear dependencies, > maybe inacurrate inversion of the overlap matrix. A way around that > problem would be to define an "intermediate basis set" by interpolating > two (preferably large) O and N basis sets that have the same contraction > pattern, ie, a "metamorphosing basis set for a metamorphosing atom". Just for fun, I tested a metamorphose of CH4 => C/NH4^{+1/2) => NH4^+, with a combined C+N TZVP basis set for C/N. It had no convergence problems at all, converging in 8-10 steps (PBE0 functional). Of course, it could get more difficult with larger molecules, and a morphed basis could be preferable. To Steve: I suffer from imagination-malfunction today; could you please give a hint on what information is gained from such a calculation :-) Have a nice day, Mikael J. http://www.helsinki.fi/~mpjohans/ From chemistry-request@ccl.net Thu Nov 6 11:17:07 2003 Received: from ned.sims.nrc.ca (ned.SIMS.nrc.ca [132.246.109.100]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6GGaVc012250 for ; Thu, 6 Nov 2003 11:16:36 -0500 Received: from ned.sims.nrc.ca (localhost [127.0.0.1]) by ned.sims.nrc.ca (8.12.6/8.12.6/SuSE Linux 0.6) with ESMTP id hA6GGZW1028441; Thu, 6 Nov 2003 11:16:35 -0500 Received: from localhost (ps@localhost) by ned.sims.nrc.ca (8.12.6/8.12.6/Submit) with ESMTP id hA6GGZMW028438; Thu, 6 Nov 2003 11:16:35 -0500 Date: Thu, 6 Nov 2003 11:16:35 -0500 (EST) From: Serguei Patchkovskii Reply-To: Serguei.Patchkovskii^at^nrc.ca To: Rene Fournier - 1999-07-07 cc: CHEMISTRY^at^ccl.net Subject: Re: CCL:fractional nuclear charge In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Virus-Scanned: by AMaViS - amavis-milter (http://www.amavis.org/) X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT, REPLY_WITH_QUOTES,USER_AGENT_PINE version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) On Thu, 6 Nov 2003, Rene Fournier - 1999-07-07 wrote: > I have a related question: does anyone know of a program that would > allow to use positive charge distributions other than a set of point > charges, for instance, a set of spherical Gaussian distributions. ADF will support an arbitrary external potential, as long as you are willing to write a routine calculating the potential at grid points. Serguei --- Dr. Serguei Patchkovskii Tel: +1-(613)-990-0945 Fax: +1-(613)-947-2838 E-mail: Serguei.Patchkovskii^at^nrc.ca Coordinator of Modelling Software Theory and Computation Group Steacie Institute for Molecular Sciences National Research Council Canada Room 2011, 100 Sussex Drive Ottawa, Ontario K1A 0R6 Canada From chemistry-request@ccl.net Thu Nov 6 10:41:21 2003 Received: from ms-smtp-02-eri0.southeast.rr.com (ms-smtp-02-lbl.southeast.rr.com [24.25.9.101]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6FeoVc011430 for ; Thu, 6 Nov 2003 10:40:50 -0500 Received: from bobcat (rdu26-84-136.nc.rr.com [66.26.84.136]) by ms-smtp-02-eri0.southeast.rr.com (8.12.10/8.12.7) with ESMTP id hA6FekLn016144; Thu, 6 Nov 2003 10:40:48 -0500 (EST) Message-ID: <005601c3a47c$52b305f0$88541a42@bobcat> From: "Robert Duke" To: "CCL" , "Jim Phillips" References: Subject: Re: CCL:PMEMD 3.1 Release - High Scalability Update to PMEMD Date: Thu, 6 Nov 2003 10:40:35 -0500 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 7bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4807.1700 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 X-Virus-Scanned: Symantec AntiVirus Scan Engine X-Spam-Status: No, hits=-1.0 required=7.0 tests=ORIGINAL_MESSAGE,QUOTED_EMAIL_TEXT, RCVD_IN_UNCONFIRMED_DSBL,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Jim - All I can say is WOW!!! That is really fantastic scaling on the JAC benchmark (I have deleted all but the benchmark data in the copy of your mail below). I am actually very impressed by two things in NAMD 2.5, based on this benchmark. First, there is the clearly superior high end scaling; I think you all have bested your previous (2.4) high end scaling performance by something like a factor of 2. Second, you all have basically also doubled the performance relative to NAMD 2.4 at the low processor count. I had previously had great respect for your scaling, but had considered that you all were not paying enough attention to performance on small numbers of processors. Not any more. This small numbers of processors performance issue is really very important; lots of folks out there have to do their runs on 4-16 cpu's. So right now, I suspect you all have the scaling title, and also about equal performance at the low end. My first reaction to the scaling was "it must be the elan optimizations on lemieux". However, on second thought, more is going on, based on my current understanding of your architecture. With your concept of cycles, you manage to make complete exchange of coordinates occur less frequently (once every 20 steps by default, I think). I do complete exchange of coordinates at pairlist builds, which is typically once every 4 to 7 steps. I guess I see a clear direction for PMEMD 3.11. Stay tuned. I think this is currently a very healthy competition, and users of both products will benefit. I need to check with Lalith and Lee, but presumably we can make the FIX benchmark more public. Congratulations again to the NAMD 2.5 team on a job well done! Regards - Bob ----- Original Message ----- From: "Jim Phillips" To: "Robert Duke" Cc: Sent: Wednesday, November 05, 2003 9:35 PM Subject: CCL:PMEMD 3.1 Release - High Scalability Update to PMEMD < other stuff deleted> > I've just done the same with the NAMD 2.5 released binary. NAMD 2.5 > dynamically adjusts pairlistdist (and temporarily and locally disables > pairlists in the case of a violation), so I started it at 10A (9A cutoff). > This is the time on Lemeiux from the last 1000 steps of a 4000 step run, > using the direct Elan implementation of Charm++ and the "+strategy > USE_MESH" command line option: > > nodes procs time (s) > > 1 4 222.122 > 2 8 115.277 > 4 16 59.4164 > 8 32 34.3925 > 16 64 22.2451 > 32 128 12.8739 > 64 256 9.90325 > > I'll leave your data below for comparison. The first surprise is that for > such different programs (FORTRAN 90 vs C++) the 4 processor times are > shockingly similar, and the race is tied up to 64 processors. However, > NAMD continues scaling up to 128 processors, at which point we hit the > frustrating 10ms/step barrier. I've skipped the academic exercise of > running fewer processors per node, and this isn't the right forum to > discuss the fundamental limits of the machine (SC 2003 in two weeks is). > For NAMD the 50% mark is at about 128 CPUs. > > > JAC Benchmark, 23558 atoms on lemieux.psc.edu, results in wall clock seconds > > per 1000 steps. > > > > #cpu #nodes PMEMD 3.1 wc sec NAMD 2.4 wc sec PMEMD/NAMD speedup > > > > 1 1 828.5 1385 1.67x > > 2 1 431.5 750 1.74x > > 4 1 218.25 390 1.79x > > 8 2 118.5 198 1.67x > > 16 4 67.25 105 1.56x > > 32 8 37 61 1.65x > > 64 16 22.25 40 1.80x > > 72 24 19 nd nd > > 96 32 17.75 nd nd > > 120 40 18.75 nd nd > > 128 32 22 23 1.05 > > In any case, competition is healthy and PMEMD is certainly a worthy and > welcome competitor for NAMD. > > Stay tuned to CCL for NAMD FIX benchmark results on the HPCx (EPCC) SP. > > -Jim > > > > -= 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 Nov 6 11:41:31 2003 Received: from mercure.neokimia.com (mercure.med.usherbrooke.ca [132.210.158.207]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6Gf0Vc012884 for ; Thu, 6 Nov 2003 11:41:00 -0500 Content-Class: urn:content-classes:message Subject: CCL:RE: clustering database molecules MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 6 Nov 2003 11:40:58 -0500 X-MimeOLE: Produced By Microsoft Exchange V6.0.6249.0 Message-ID: X-MS-Has-Attach: X-MS-TNEF-Correlator: Thread-Topic: CCL:RE: clustering database molecules Thread-Index: AcOkgGChwe+OOzJTQGSJKXEG0yb1BAAAB++A From: "Axel Mathieu" To: "Joey Harriman" Cc: 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) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hA6GfVVc012974 Hello Joey, I'm working with MOE and have used MOE:Similarity to cluster similar conformations. Our molecules are semi-peptidic macrocycles (about 40-50 atoms) and thus should be somewhat similar to your system. I've had success using Typed Atom Triangles (3D fingerprints) with a Tanimoto coefficient of 90%. Unfortunately, MOE:Similarity does not really cluster and/or does not make the results in a transferable data format such as to obtain the results without repetitively manually creating new files. I therefore proceeded in creating a script that uses MOE:Similarity to report the number of different families, the number of similar conformers within a family, export the separated families into new databases, and can even pipe the whole thing to population analyses. I only came up with a Tanimoto coefficient of 90% by trial and error (my modified scripts helped of course) obviously dependant on my definition of a cluster and what defines a new family. So, I suggest you do the same thing ... Say HI to Ghislain Deslongchamps, Rod Cooper, and Larry Calhoun for me ... ;O) Axel -----Original Message----- From: Joey Harriman [mailto:s808o)at(unb.ca] Sent: 6 novembre, 2003 10:14 To: CCL posting Subject: CCL:clustering database molecules Hi, I am trying to cluster a database of a tetrapeptide with different geometries. I am currently using MOE and have tried varying fingerprints (at the 99%) threshold with no success. Does anyone have a good system for clustering different geometries of the same molecule from a database? Thanks in advance for any help you can offer. Joey ---------------------------------- Joey Harriman MSc Computational Chemistry University of New Brunswick Room 228 Toole Hall s808o)at(unb.ca 476-6543 ---------------------------------- -= 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 Nov 6 12:29:20 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 hA6HSmVc014112 for ; Thu, 6 Nov 2003 12:28:48 -0500 Received: (from hlwoodc@localhost) by helix.nih.gov (8.11.7-8.359.2.8/8.11.6) id hA6HSjm41082890; Thu, 6 Nov 2003 12:28:45 -0500 (EST) Date: Thu, 6 Nov 2003 12:28:44 -0500 From: Lee Woodcock To: Rene Fournier - 1999-07-07 cc: Mikael Johansson , Steve Williams , CHEMISTRY!at!ccl.net Subject: Re: CCL:fractional nuclear charge In-Reply-To: Message-ID: References: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=-2.0 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,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) On Thu, 6 Nov 2003, Rene Fournier - 1999-07-07 wrote: > >I have a related question: does anyone know of a program that would >allow to use positive charge distributions other than a set of point >charges, for instance, a set of spherical Gaussian distributions. > Gamess-Uk does this. Take a look at the following article... Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method, JOURNAL OF CHEMICAL PHYSICS, Volume 117, Issue 23, 15 Dec. 2003, Pages 10534-10547, Das D, Eurenius, KP, Billings, EM, Sherwood, P, Chatfield, DC, Hodoscek, M, Brooks, BR Cheers, Lee Woodcock, Ph.D. --------------- hlwood!at!nih.gov --------------- From chemistry-request@ccl.net Thu Nov 6 10:56:20 2003 Received: from mailserver.unimi.it (mailserver.unimi.it [159.149.10.5]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6FtmVc011750 for ; Thu, 6 Nov 2003 10:55:49 -0500 Received: from smtp.unimi.it (smtp.unimi.it [159.149.10.3]) by mailserver.unimi.it (iPlanet Messaging Server 5.2 Patch 1 (built Aug 19 2002)) with ESMTP id <0HNX002ETTL1PR!at!mailserver.unimi.it> for chemistry!at!ccl.net; Thu, 06 Nov 2003 16:55:50 +0100 (MET) Received: from heisenberg.chimica.unimi.it (heisenberg.chimica.unimi.it [159.149.240.30]) by smtp.unimi.it (iPlanet Messaging Server 5.1 (built May 7 2001)) with ESMTP id <0HNX00M5UTKY9Q!at!smtp.unimi.it> for chemistry!at!ccl.net; Thu, 06 Nov 2003 16:55:46 +0100 (MET) Received: by heisenberg.chimica.unimi.it (Postfix, from userid 500) id A2982320AE; Thu, 06 Nov 2003 17:07:12 +0100 (CET) Received: from localhost (localhost [127.0.0.1]) by heisenberg.chimica.unimi.it (Postfix) with ESMTP id 92F38320AD for ; Thu, 06 Nov 2003 17:07:12 +0100 (CET) Date: Thu, 06 Nov 2003 17:07:11 +0100 (CET) From: Alessandro Contini Subject: summary mp2/cc-pvtz To: chemistry!at!ccl.net Message-id: MIME-version: 1.0 Content-type: TEXT/PLAIN; charset=ISO-8859-1 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) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from QUOTED-PRINTABLE to 8bit by server.ccl.net id hA6FuKVc011763 Hi, I'd like to thanks Marcel Swart, Stephen Garrison, Olga Dmitrenko and Giovanni Scalmani for the kind reply. The problem as suggested was derived by a "out of disk" or "out of memory" error (the famous -1); however I could not solve it because the disk requested for my system was 280GB and more for a semidirect and at least 25GB of memory for a direct optimization. However the calculation run properly with B3LYP/cc-pvtz, B3LYP/tzvp and B3LYP/6-311+G(2d,p) basis. Thanks again Alessandro Contini Alessandro Contini, Ph.D. Istituto di Chimica Organica "Alessandro Marchesini" Universit` degli Studi di Milano, Facolt` di Farmacia Via Venezian, 21 20133 Milano Tel. +390250314480 Fax. +390250314476 e-mail alessandro.contini!at!unimi.it From chemistry-request@ccl.net Thu Nov 6 12:35:28 2003 Received: from lgdx04.lg.ehu.es (lgdx04.lg.ehu.es [158.227.1.36]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6HYsVc014320 for ; Thu, 6 Nov 2003 12:34:55 -0500 Received: by lgdx04.lg.ehu.es id SAA0000016792; Thu, 6 Nov 2003 18:34:51 +0100 (MET) Message-ID: <007901c3a48c$4789dd60$222fe39e..at..lc.ehu.es> From: "Pablo Vitoria" To: "Close, David M." , "CCL" References: Subject: Re: CCL:Dual Xeon G98 Summary Date: Thu, 6 Nov 2003 18:34:49 +0100 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0076_01C3A494.A93D7C80" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 6.00.2800.1158 X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=-0.3 required=7.0 tests=HTML_60_70,HTML_MESSAGE,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0076_01C3A494.A93D7C80 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear Dave, I am sorry I didn't answer before, I guess I missed your previos = message. The command "echo "356515840" >/proc/sys/kernel/shmmax" is fine and it = works, but you will have to enter it after every restart of the = computer. In Mandrake (that's what I use, but I guess is the same in = other distros) I would add a line like: kernel.shmmax=3D356515840 to the file /etc/sysctl.conf, so that it's read at every restart of the = machine. Best regards Pablo -------------------------------------------------------- Pablo Vitoria Garcia Dpto. Qu=EDmica Inorg=E1nica, Facultad de Ciencias Universidad del Pa=EDs Vasco (UPV/EHU) Aptdo. 644 48080 Bilbao (Bizkaia) Tfno. 94 6015992 Fax. 94 4648500 ----- Original Message -----=20 From: Close, David M.=20 To: chemistry..at..ccl.net=20 Sent: Thursday, November 06, 2003 1:32 AM Subject: CCL:Dual Xeon G98 Summary CCL'ers: Thanks so much for the quick replies. I have the system working = now. Some who wrote me asked questions like, Was I logged in as root?, = and did I have the SMP Kernel loaded? Also some thought that LINDA was needed to run 2 processors on a = "parallel" job. This is not the case however. The answer was simply to balance the "bytes" read into shmmax with = the %mem=3D line in the input file. So for my 512 Mb total memory and 2 processors, the suggestion was = to put 2/3 of available memory as shared memory. So 340 Mb is 356515840 = bytes. =20 This is done with echo "356515840" >/proc/sys/kernel/shmmax. =20 I ran a test job of an OPT on the N1-H deprotonated cytosine cation = with B3LYP/6-31+G(d) which took 3 hours and 18 minutes with a single = processor and 1 hour 51 minutes with %Nproc=3D2. That's 1.78 times = faster. =20 I thank everyone who help out with this. Regards, Dave Close. =20 ------=_NextPart_000_0076_01C3A494.A93D7C80 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Dear Dave,
 
I am sorry I didn't answer before, I = guess I missed=20 your previos message.
 
The command  "echo =93356515840=94 = >/proc/sys/kernel/shmmax" is fine and it works, but you will have to = enter it=20 after every restart of the computer. In Mandrake (that's what I use, but = I guess=20 is the same in other distros) I would add a line like:
 
kernel.shmmax=3D356515840
 
to the file /etc/sysctl.conf, so that = it's read at=20 every restart of the machine.
 
Best regards
 
Pablo
--------------------------------------------------------
Pablo = Vitoria=20 Garcia
Dpto. Qu=EDmica Inorg=E1nica, Facultad de = Ciencias
Universidad del Pa=EDs=20 Vasco (UPV/EHU)
Aptdo. 644
48080 Bilbao (Bizkaia)
 
Tfno. 94 6015992
Fax. 94 4648500
----- Original Message -----
From:=20 Close, David=20 M.
Sent: Thursday, November 06, = 2003 1:32=20 AM
Subject: CCL:Dual Xeon G98 = Summary

  = CCL=92ers:

    Thanks so much = for the=20 quick replies.  I have = the system=20 working now.

  Some who wrote me asked = questions=20 like, Was I logged in as root?, and did I have the SMP Kernel=20 loaded?

  Also some thought that LINDA = was=20 needed to run 2 processors on a =93parallel=94 job.  This is not the case=20 however.

  The answer was simply to = balance the=20 =93bytes=94 read into shmmax with the %mem=3D line in the input=20 file.

  So for my 512 Mb total = memory and 2=20 processors, the suggestion was to put 2/3 of available memory as = shared=20 memory.  So 340 Mb is = 356515840=20 bytes.

 

  This is done with echo = =93356515840=94=20 >/proc/sys/kernel/shmmax.

 

  I ran a test job of an OPT = on the N1-H=20 deprotonated cytosine cation with B3LYP/6-31+G(d) which took 3 hours = and 18=20 minutes with a single processor and 1 hour 51 minutes with %Nproc=3D2. = That=92s=20 1.78 times faster.

 

  I thank everyone who help = out with=20 this.

  Regards, Dave=20 Close.

 

------=_NextPart_000_0076_01C3A494.A93D7C80-- From chemistry-request@ccl.net Thu Nov 6 15:08:16 2003 Received: from cornell.edu (cornell.edu [132.236.56.6]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6K7jVc018407 for ; Thu, 6 Nov 2003 15:07:45 -0500 Received: from cwlaptop (syr-24-169-77-71.twcny.rr.com [24.169.77.71]) by cornell.edu (8.9.3p2/8.9.3) with SMTP id PAA15830 for ; Thu, 6 Nov 2003 15:07:45 -0500 (EST) Message-ID: <000801c3a4cb$88d4ce30$0701a8c0@cwlaptop> From: "Connie Chang" To: Subject: CCL: Gaussian03 DFT Freq error Date: Thu, 6 Nov 2003 20:07:36 -0500 MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_0005_01C3A4A1.9F7CEC00" X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.50.4522.1200 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4522.1200 X-Spam-Status: No, hits=2.8 required=7.0 tests=DATE_IN_FUTURE_03_06,FROM_ENDS_IN_NUMS,HTML_40_50, HTML_MESSAGE version=2.55 X-Spam-Level: ** X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) This is a multi-part message in MIME format. ------=_NextPart_000_0005_01C3A4A1.9F7CEC00 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi : I am using Gaussian03 for a 72 atom molecule, DFT with this route #BLYP 6-21G SCF=3D(MaxCyc=3D2000) Opt Freq Test The optimization completed, but the frequency job ends early with this = error: What does the error mean and how can I correct it? Requested convergence on RMS density matrix=3D1.00D-08 within2000 = cycles. Requested convergence on MAX density matrix=3D1.00D-06. Requested convergence on energy=3D1.00D-06. No special actions if energy rises. SCF Done: E(RB-LYP) =3D -2739.18562154 A.U. after 1 cycles Convg =3D 0.6724D-09 -V/T =3D 2.0052 S**2 =3D 0.0000 Range of M.O.s used for correlation: 1 648 NBasis=3D 648 NAE=3D 216 NBE=3D 216 NFC=3D 0 NFV=3D 0 NROrb=3D 648 NOA=3D 216 NOB=3D 216 NVA=3D 432 NVB=3D 432 **** Warning!!: The smallest alpha delta epsilon is 0.22458850D-01 Write error in NtrExt1 THanks, COnnie ------=_NextPart_000_0005_01C3A4A1.9F7CEC00 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi :
 
I am using Gaussian03 for a 72 atom = molecule, DFT=20 with this route
#BLYP 6-21G SCF=3D(MaxCyc=3D2000) Opt = Freq=20 Test
 
The optimization completed, but the = frequency job=20 ends early with this error:
What does the error mean and how can I = correct=20 it?
 
 
 Requested convergence on RMS = density=20 matrix=3D1.00D-08 within2000 cycles.
 Requested convergence on = MAX density=20 matrix=3D1.00D-06.
 Requested convergence=20 on            = ;=20 energy=3D1.00D-06.
 No special actions if energy = rises.
 SCF=20 Done:  E(RB-LYP) =3D  -2739.18562154     = A.U.=20 after    1=20 cycles
          &nb= sp; =20 Convg  =3D   =20 0.6724D-09          &nb= sp; =20 -V/T =3D =20 2.0052
          &nb= sp; =20 S**2   =3D   0.0000
 Range of M.O.s used for = correlation:     1  =20 648
 NBasis=3D   648 NAE=3D   216 = NBE=3D   216=20 NFC=3D     0 NFV=3D    =20 0
 NROrb=3D    648 NOA=3D   216 = NOB=3D  =20 216 NVA=3D   432 NVB=3D   432
 
 **** Warning!!: The smallest = alpha delta=20 epsilon is  0.22458850D-01
 
 Write error in = NtrExt1
 
 
THanks,
 
COnnie
------=_NextPart_000_0005_01C3A4A1.9F7CEC00-- From chemistry-request@ccl.net Thu Nov 6 17:11:16 2003 Received: from sycorax.delfa.net (relay4.delfa.net [193.125.210.9]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA6MAiVc020563 for ; Thu, 6 Nov 2003 17:10:45 -0500 X-Envelope-To: Received: from dux.ru (dux.ru [193.125.210.65]) by sycorax.delfa.net (8.12.10/8.12.10/Sycorax.Delfa) with ESMTP id hA6MAiTY027302 for ; Fri, 7 Nov 2003 01:10:44 +0300 Received: from dux.ru (localhost [127.0.0.1]) by dux.ru (8.12.6/8.12.6) with ESMTP id hA6MAh5l072555 for ; Fri, 7 Nov 2003 01:10:43 +0300 (MSK) (envelope-from dima(at)xenon.spb.ru) Received: (from uucp@localhost) by dux.ru (8.12.6/8.12.1/Submit) with UUCP id hA6MAh85072553 for chemistry(at)ccl.net; Fri, 7 Nov 2003 01:10:43 +0300 (MSK) (envelope-from dima(at)xenon.spb.ru) Received: from goblin ([192.168.5.1] helo=xenon.spb.ru ident=dima) by shadow with esmtp (Exim 3.35 #1 (Debian)) id 1AHsHZ-0006bt-00 for ; Fri, 07 Nov 2003 01:07:13 +0300 Message-ID: <3FAAC611.2030100(at)xenon.spb.ru> Date: Fri, 07 Nov 2003 01:07:13 +0300 From: Dmitry Rozmanov User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.5) Gecko/20031024 Debian/1.5-2 X-Accept-Language: ru, en MIME-Version: 1.0 To: CCL Subject: good molecular builder 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) Hello. Could anyone suggest a convenient molecular builder. My task is, say, I have optimized geometry for water and nitric anion. Then I want to compose a system using their geometries with cation, anion and 10 waters. It is enough if it saves xyz file. In fact it is preferably. Any suggestions? Everything I saw either shows molecules or offer building but from the very scratch. Thank you all in advance. Regards. ---Dmitry.