From chemistry-request@server.ccl.net Fri Jul 28 03:45:23 2000 Received: from compchem.dfh.dk (compchem.dfh.dk [130.225.225.51]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id DAA27693 for ; Fri, 28 Jul 2000 03:45:22 -0400 Received: from [130.225.225.151] (dhcp225-151.dfh.dk [130.225.225.151]) by compchem.dfh.dk (SGI-8.9.3/8.9.3) with ESMTP id JAA13159 for ; Fri, 28 Jul 2000 09:44:45 +0200 (MEST) Mime-Version: 1.0 Message-Id: In-Reply-To: <397C5C3F.28DEEEDA@eeyore.cm.utexas.edu> References: <397C5C3F.28DEEEDA@eeyore.cm.utexas.edu> Date: Fri, 28 Jul 2000 09:44:06 +0200 To: chemistry@ccl.net From: Per-Ola Norrby Subject: TM force fields Content-Type: text/plain; charset="us-ascii" ; format="flowed" Isaac B. Bersuker wrote: >I repeat my firm conviction that, in general, there are >no force fields for transitiom metal systems (see my latest book ... (The rest of the message deleted). I've seen this comment a couple of times now, and I'm getting irritated. This is a very sweeping statement, and insulting to those who have produced good work in this area. It is only true if you interprete it like "it is not possible to achieve infinite accuracy for all possible TM complexes", but stated like that it would be equally true of any method. For specific classes of complexes, it is possible to get high accuracy with force field methods. It's just a question of having a flexible enough force field and doing a careful parameterization. Check out the book by Comba and Hambley, "Molecular Modeling of Inorganic Compounds", a new edition is comming out soon. We also have a review in press in Coord.Chem.Rev. on how to do this parameterization (don't know when it's going to appear). For some classical reviews, see: C.R. Landis, D.M. Root, T. Cleveland, in: K.B. Lipkowitz and D.B. Boyd (Eds.), Reviews in Computational Chemistry, Vol. 6, VCH Publishers, Inc., New York, 1995, p. 73-148. M. Zimmer, Chem. Rev. 95 (1995) 2629. P. Comba, Comments Inorg. Chem. 16 (1994) 133. B.P. Hay, Coordination Chemistry Reviews 126 (1993) 177. (Yes, I know, I left several out, this is just a selection based on personal preference). The general force fields are also advancing. You can still get whooping errors, and should validate carefully, but I've actually been surprised several times by the results you can get without specific parameterization. I'd like to point to UFF (not all implementations though :-), VALBOND (not a complete force field, but a very interesting addition to UFF), and the force fields in PCModel and Spartan. There are others, but I don't have personal experience with them. Per-Ola -- ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ * Per-Ola Norrby, Associate Professor * The Royal Danish School of Pharmacy, Dept. of Med. Chem. * Universitetsparken 2, DK 2100 Copenhagen, Denmark * Tel. +45-35306506, fax +45-35306040 * Email: peo@dfh.dk (preferred), peo@compchem.dfh.dk * WWW: http://compchem.dfh.dk/PeO/ From chemistry-request@server.ccl.net Fri Jul 28 02:51:52 2000 Received: from hotmail.com (f54.law9.hotmail.com [64.4.9.54]) by server.ccl.net (8.8.7/8.8.7) with SMTP id CAA27515 for ; Fri, 28 Jul 2000 02:51:52 -0400 Received: (qmail 34763 invoked by uid 0); 28 Jul 2000 06:49:45 -0000 Message-ID: <20000728064945.34762.qmail@hotmail.com> Received: from 203.28.79.34 by www.hotmail.com with HTTP; Thu, 27 Jul 2000 23:49:45 PDT X-Originating-IP: [203.28.79.34] From: "Henry Pang" To: hocquet@hotmail.com Cc: CHEMISTRY@ccl.net Subject: Re: CCL:philosophy of computational chemistry" Date: Fri, 28 Jul 2000 06:49:45 GMT Mime-Version: 1.0 Content-Type: text/plain; format=flowed Hi Alexandre Do tell me what is your 'sociological manner'. My approach to the Philosophy of CC appeared recently. Let me copy in case you missed it. July 26 2000 CCL Hi David, greetings to Dr Buyong Ma You said You discern correctly. Buyong Ma (1995), is refreshing because addressing the wider nature of CC within the environment of science, but different to my concern. My point of departure is me. The most vital concern in my life is me. I want to survive so I can address other things. To survive in real terms, I want to develop a holistic integrated view of of reality. The basic unit is the system of the infinity of universes beyond our home Universe. In hierarchal form, all the fields we know as disciplines, are not isolated things but are linked otherwise they would disintegrate. I mean the Milky Way, solar system, planet earth, biosphere, living things, homo sapiens and so on. The key instruments which explore reality at this time, include cosmology, quantum theory, relativity and higher dimensions theory. Astronomy appears to merely catalogue the celestial bodies. I have yet to see an astronomer discuss why these bodies exist in the heavens? When I was introduced to CC, I was delighted because I naively thought the precision, the 3D and the associated computational power would produce essential data for my Universe model? Alas, like the astronomers, CC seems only concerned with the means and not the ends. CC is intensely focussed on computer programs and delights in addressing techniques. There are a few bold warriors apart from Buyong Ma (1995). Stephen Mason(1991), Chemical Evolution - Origins of the Elements, Molecules and Living Systems, Clarendon Press Oxford, but closer to my vision - Pierre Teilhard de Chardin (1955), The Phenomenon of Man, Fontana Books. Review by Arnold Toynee Observer - I believe computational chemistry is more than mere mensuration and rotating images. I am sure molecules were created as the essential building blocks of the infinite universe system. I want to set out the physical, mental, social and spiritual nature of living things and our Universe. I am intensely interested in Origins? I am sure the findings of CC form an important part of this unfolding story. Dr Henry Pang Postgraduate Student, Computational Chemistry Faculty of Science, Information Technology and Education Northern Territory University PO Box U273 NT University 0815 Australia Mobile 0419 682121 Fax 61 8 8946 6847 hpangaus@hotmail.com >From: "Alexandre Hocquet" >To: jsl@virgil.ruc.dk >CC: chemistry@ccl.net >Subject: CCL:philosophy of computational chemistry" >Date: Wed, 26 Jul 2000 23:06:14 GMT > > >dear jens, >You may be interested in the last release of the journal "foundations of >chemistry" (i dont have the exact reference but you may find it at >http://www.wkap.nl/journalhome.htm/1386-4238). Its editor in chief, eric >scerri, deals with the subject of "molecular orbital vision". > >Your argued your point was not philosophical but for the people that are >interested : > >Talking about philosophy of computational chemistry, this journal is >certainly an interesting resource as can be Hyle >(http://www.uni-karlsruhe.de/~philosophie/hyle.html), edited by Joachim >Schummer. These two young journals deal with philosophical aspects of >chemistry from the point of view of chemists AND philosophers and some >articles deal with theoretical and computational chemistry. Another >valuable resource is the PHILCHEM mailing list ( >http://www.cla.sc.edu/Phil/faculty/baird/philch.htm). > >Last, i am myself in the process of adressing the subject of a "philosophy >of computational chemistry" in a sociological manner. i intend to ask the >CCLers what they think (this will be done in september, to maximise >response) by asking to fill a questionnaire, just like i did it in June at >the ICQC (International Conference on Quantum Chemistry) in Menton. The >results will be submitted for publication in one of the two mentionned >journals. I can send to anyone interested the abstract of the poster >accompanying the survey in Menton. > >Sincerely, > >------------------------------------------------------------ >Alexandre HOCQUET >Laboratoire de Physicochimie Biomoléculaire et Cellulaire >ESA CNRS 7033 >hocquet@lpbc.jussieu.fr >Fax: 0144277560 >(do not dial first 0 from abroad) >LPBC, case courrier 138 >4 Place Jussieu, 75252 PARIS Cedex 05 France >------------------------------------------------------------ > > >________________________________________________________________________ >Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com > > > >-= This is automatically added to each message by mailing script =- >CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To >Admins >MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH >CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net >70 >Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: >jkl@ccl.net > > > > > ________________________________________________________________________ Get Your Private, Free E-mail from MSN Hotmail at http://www.hotmail.com From chemistry-request@server.ccl.net Fri Jul 28 11:06:44 2000 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.8.7/8.8.7) with SMTP id LAA30382 for ; Fri, 28 Jul 2000 11:06:44 -0400 From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 8625692A.0052FD71 ; Fri, 28 Jul 2000 10:06:28 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: chemistry@ccl.net Message-ID: <8625692A.0052FC86.00@unomail.unomaha.edu> Date: Fri, 28 Jul 2000 10:06:24 -0500 Subject: Compiling G94 on Mandrake Linux Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline In setting up a Dual Pentium Pro PC to run G94 under the Linux OS, we run into problems when trying to compile G94, rev. E. The OS is Linux kernel 2.2.15 using the Mandrake distribution. I know that Mandrake is suppose to use much of Redhat's code in the version of Linux, but I sure wish I would have installed Redhat's latest kernel, I have many problems with the Mandrake installation, but that's another story. The PC is a Micron Dual Pentium Pro box. I had G94 compile successfully on this box using Redhat Linux ver. 5.1 when running just one processor. This successful compilation was done just as instructed via the G94 manual using the f2c/gcc compiler combo. But now, with Mandrake 7.1, and using dual processors (the kernel has been compiled with the SMP option on), the compilation process stops after making link 401. All executables up to l401 are made (and work), but the process stops at link 402. Any ideas? I search the CCL archives to find past discussion on compiling G94 on Dual Pro PCs, but I'm well versed in compilers and the different flags people have tried. Does anyone have a g94.make file that they have used to compile a Dual Pentium Pro machine under Linux. Are the latest versions of f2c/gcc not compatible with G94? Would the Portland compiler work on a dual Pentium Pro PC in compiling G98? Any advice (esp. if Doug Fox is listening) would be appreciated! Douglas E. Stack Assistant Professor University of Nebraska at Omaha Department of Chemistry Omaha, NE 68182-0109 (402) 554-3647 (voice) (402) 554-3888 (FAX) destack@unomaha.edu From chemistry-request@server.ccl.net Fri Jul 28 14:23:08 2000 Received: from usintout01.net.bms.com (usintout01.bms.com [165.89.129.231]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id OAA31790 for ; Fri, 28 Jul 2000 14:23:08 -0400 Received: from nsusmsg03.net.bms.com ([127.0.0.1]) by mochilla.bms.com (PMDF V5.2-32 #38481) with ESMTP id <0FYF00DBO72KIU@mochilla.bms.com> for chemistry@ccl.net; Fri, 28 Jul 2000 18:23:08 +0000 (GMT) Received: from bms.com ([140.176.4.156]) by nsusmsg03.net.bms.com (Netscape Messaging Server 4.15) with ESMTP id FYF72K00.8I8 for ; Fri, 28 Jul 2000 18:23:08 +0000 Date: Fri, 28 Jul 2000 14:23:02 -0400 From: Andrew T Pudzianowski Subject: Prediction of fluorescence? To: chemistry@ccl.net Message-id: <3981CF86.D265AD2B@bms.com> Organization: Bristol-Myers Squibb MIME-version: 1.0 X-Mailer: Mozilla 4.5 [en]C-BMY (WinNT; U) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit X-Accept-Language: en Hello and happy Friday (to everyone in an appropriate time zone)! Does anybody have any experience with or knowledge of schemes for predicting fluorescence in the UV/visible range for a given set of molecules? I can't think of any reliable theoretical scheme for deciding whether a given electronic transition will give rise to fluorescence, but it's been a long time since I've thought about such things! All positive responses will included in a summary. Regards, Andrew Pudzianowski Computer-Assisted Drug Design Bristol-Myers Squibb PRI Princeton NJ From chemistry-request@server.ccl.net Fri Jul 28 14:46:52 2000 Received: from unomail.unomaha.edu (unomail.unomaha.edu [137.48.1.6]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA31962 for ; Fri, 28 Jul 2000 14:46:52 -0400 From: Douglas_Stack/CAS/UNO/UNEBR@unomail.unomaha.edu Received: by unomail.unomaha.edu(Lotus SMTP MTA v4.6.4 (830.2 3-23-1999)) id 8625692A.00672A6E ; Fri, 28 Jul 2000 13:46:50 -0500 X-Lotus-FromDomain: UNIVERSITY OF NEBRASKA To: chemistry@ccl.net cc: John Flocken , Frank_Hartranft/CAS/UNO/UNEBR@unomail.unomaha.edu Message-ID: <8625692A.0067289D.00@unomail.unomaha.edu> Date: Fri, 28 Jul 2000 13:46:45 -0500 Mime-Version: 1.0 Content-type: text/plain; charset=us-ascii Content-Disposition: inline Dear CCLers, Our University has an established computational laboratory which was funded by a one-time NSF grant. It consists of an SGI Onyx Cray-linked to an SGI Origin 2000 (24 total CPUs). As the original NSF grant is about to expire, we developing policies to fund this lab from individual, faculty grants. My question is: how does one fund a computation lab from individual users? A flat, per-year charge, by CPU time, etc.? Since the budget of any grant is an important component in the funding decision, we want to make sure the requests are reasonable. The funds would be used to pay for support staff (sys. admin.) and occasional hardware/software upgrades. If any on you have current funding polices in place, we would be grateful if could share them with us so that we can build on your experiences. In addition, if any of you have recently been involved in a grant review study section reviewing computational proposals, what type of charges did you find reasonable (any maybe just as important, what was considered unreasonable). As always, thanks in advance. Douglas E. Stack Assistant Professor University of Nebraska at Omaha Department of Chemistry Omaha, NE 68182-0109 (402) 554-3647 (voice) (402) 554-3888 (FAX) destack@unomaha.edu From chemistry-request@server.ccl.net Fri Jul 28 13:39:40 2000 Received: from Post-Office.UH.EDU (Post-Office.UH.EDU [129.7.1.20]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id NAA31608 for ; Fri, 28 Jul 2000 13:39:39 -0400 Received: from CONVERSION-DAEMON by Post-Office.UH.EDU (PMDF V5.2-32 #40812) id <0FYF00L0151LS9@Post-Office.UH.EDU> for chemistry@ccl.net; Fri, 28 Jul 2000 12:39:22 -0500 (CDT) Received: from uh.edu (Kroll.BCHS.UH.EDU [129.7.2.217]) by Post-Office.UH.EDU (PMDF V5.2-32 #40812) with ESMTP id <0FYF00LPB51LVE@Post-Office.UH.EDU>; Fri, 28 Jul 2000 12:39:21 -0500 (CDT) Date: Fri, 28 Jul 2000 12:39:55 -0500 From: Joe Huang Subject: Error message in CHARMM: RESIDUE NUMBER OVERFLOW! To: charmm-bbs@csir.org, chemistry@ccl.net Message-id: <3981C56B.5F58B41F@uh.edu> Organization: BCHS, UH MIME-version: 1.0 X-Mailer: Mozilla 4.7 [en] (Win98; I) Content-type: multipart/mixed; boundary="Boundary_(ID_cWuroSsyaf5c7h17f7bAbw)" X-Accept-Language: en This is a multi-part message in MIME format. --Boundary_(ID_cWuroSsyaf5c7h17f7bAbw) Content-type: text/plain; charset=us-ascii Content-transfer-encoding: 7bit Hi, dear computational chemist: I have a very big system (~60K atoms) running MD with CHARMM(c26b1) and this is the second time I encounter this kind of error message. When I got this error message long time ago, some people suggested me to recompile a bigger CHARMM version and(or) reduce the frequency for IMGFRQ; I did recompile a bigger CHARMM version (2 times the size of large version) and the MD simulation could be continued afterward. But, now, after 60000 steps of simulations in production phase (2 fs timestep with SHAKE), I encounter this error message again! This time, I don't think I should recompile CHARMM because I must allocate more swap spaces or add more physical memories for bigger CHARMM to run in our Linux Beowulf cluster (from last time's experience). I do need to find the real problem. The error message (last part of the output file) is attached. Can anybody give me some help for this problem. Thanks!!! Joe http://adrik.bchs.uh.edu/~jhuang --Boundary_(ID_cWuroSsyaf5c7h17f7bAbw) Content-type: text/plain; charset=us-ascii; name="error.txt" Content-disposition: inline; filename="error.txt" Content-transfer-encoding: 7bit DYNA> 10100 176.20000-145196.56906 37139.79273-182336.36179 298.97610 DYNA PROP> 22.58034-145014.87705 37658.91794 181.69200 52734.21802 DYNA INTERN> 22279.30550 16050.18997 784.84713 4162.75579 356.52905 DYNA EXTERN> 12445.17922-167441.47343 .00000 .00000 .00000 DYNA IMAGES> 8671.74361 -79645.43862 .00000 .00000 .00000 DYNA PRESS> -8987.68123 -26168.46411 1098.00810 -131.26582 561261.49789 DYNA XTLE> -84726.66395 47.50944 60452.92867 146.80789 ---------- --------- --------- --------- --------- --------- Crystal Parameters : Crystal Type = ORTH DYNA A = 74.29847 B = 103.10938 C = 73.26342 DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 DYNA PIXX = -75.76 PIYY = -347.14 PIZZ = 29.10 DYNA PIXY = 116.57 PIXZ = 136.97 PIYZ = -221.35 DYNA Gradient Norm = 186.93365 DYNAMC> Averages for the last 100 steps: AVER DYN: Step Time TOTEner TOTKe ENERgy TEMPerature AVER PROP: GRMS HFCTote HFCKe EHFCor VIRKe AVER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers AVER EXTERN: VDWaals ELEC HBONds ASP USER AVER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec AVER PRESS: VIRE VIRI PRESSE PRESSI VOLUme AVER XTLE: XTLTe SURFtension XTLPe XTLtemp ---------- --------- --------- --------- --------- --------- AVER> 100 176.20000-144993.22089 37264.30228-182257.52317 299.97840 AVER PROP> 22.57498-144822.28572 37768.93365 170.93517 37694.52255 AVER INTERN> 22297.86430 16075.33709 774.60331 4175.84117 376.62798 AVER EXTERN> 12567.49870-167642.68587 .00000 .00000 .00000 AVER IMAGES> 8708.61650 -79591.22635 .00000 .00000 .00000 AVER PRESS> -602.73034 -24526.95136 73.70963 79.43785 560849.69639 AVER XTLE> -84784.53011 -8.71134 60203.97251 330.49902 ---------- --------- --------- --------- --------- --------- Lattice Parameters> Averages for the last 100 steps: Crystal Parameters : Crystal Type = ORTH AVER A = 74.29227 B = 103.15675 C = 73.18218 AVER Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 AVER PIXX = 140.50 PIYY = 32.20 PIZZ = 65.62 AVER PIXY = -4.21 PIXZ = 58.57 PIYZ = -24.21 AVER Gradient Norm = 162.67136 DYNAMC> RMS fluctuations for the last 100 steps: FLUC> 100 176.20000 250.20486 149.42893 207.12762 1.20291 FLUC PROP> .03378 249.42746 145.12242 35.65197 12307.05905 FLUC INTERN> 33.93377 48.07946 11.16401 26.29130 16.14529 FLUC EXTERN> 154.09754 245.27650 .00000 .00000 .00000 FLUC IMAGES> 98.65660 164.99461 .00000 .00000 .00000 FLUC PRESS> 8282.34822 1115.50770 1012.58138 139.17979 217.20379 FLUC XTLE> 43.70536 61.91745 289.94303 207.26611 ---------- --------- --------- --------- --------- --------- Lattice Parameters> RMS fluctuations for the last 100 steps: Crystal Parameters : Crystal Type = ORTH FLUC A = .02949 B = .03290 C = .04172 FLUC Alpha = .00000 Beta = .00000 Gamma = .00000 FLUC PIXX = 234.62 PIYY = 141.25 PIZZ = 184.24 FLUC PIXY = 158.16 PIXZ = 93.54 PIYZ = 153.53 FLUC Gradient Norm = 50.05679 DYNAMC> Averages for the last 60100 steps: LAVE> 60100 176.20000-144728.50534 37267.45873-181995.96407 300.00381 LAVE PROP> 22.59728-144560.06417 37772.73337 168.44117 37765.78738 LAVE INTERN> 22309.65420 16135.51400 779.89648 4203.57423 375.80605 LAVE EXTERN> 14973.91500-188098.58100 .00000 .00000 .00000 LAVE IMAGES> 6242.94376 -58918.68678 .00000 .00000 .00000 LAVE PRESS> -11.63644 -25165.55514 1.59627 2.12337 562963.54364 LAVE XTLE> -113863.41725 1.69350 30864.29608 305.77406 ---------- --------- --------- --------- --------- --------- Lattice Parameters> Averages for the last 60100 steps: Crystal Parameters : Crystal Type = ORTH LAVE A = 73.98858 B = 103.30068 C = 73.65766 LAVE Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 LAVE PIXX = -.17 PIYY = 1.33 PIZZ = 5.22 LAVE PIXY = .91 PIXZ = .43 PIYZ = -7.62 LAVE Gradient Norm = 156.71433 DYNAMC> RMS fluctuations for the last 60100 steps: LFLC> 60100 176.20000 337.15987 147.63725 301.99156 1.18848 LFLC PROP> .03798 335.11167 144.38475 34.23740 12128.31420 LFLC INTERN> 43.36087 71.47672 14.15320 41.68994 13.70573 LFLC EXTERN> 1817.84088 14516.75251 .00000 .00000 .00000 LFLC IMAGES> 1751.03065 14562.24764 .00000 .00000 .00000 LFLC PRESS> 8109.73278 1300.80780 988.58605 158.15202 3075.38226 LFLC XTLE> 16783.10210 88.53178 16957.98651 277.38039 ---------- --------- --------- --------- --------- --------- Lattice Parameters> RMS fluctuations for the last 60100 steps: Crystal Parameters : Crystal Type = ORTH LFLC A = .31254 B = .28508 C = .39783 LFLC Alpha = .00000 Beta = .00000 Gamma = .00000 LFLC PIXX = 220.40 PIYY = 225.02 PIZZ = 224.97 LFLC PIXY = 137.45 PIXZ = 138.34 PIYZ = 138.08 LFLC Gradient Norm = 71.16777 DRIFT/STEP (LAST-TOTAL): -5.1396250 -9.97683497E-03 E AT STEP 0 : -144562.73 -144260.26 CORR. COEFFICIENT : -.59480529 -.51651993 UPDECI: Image update at step 10100 UPDECI: Nonbond update at step 10100 UPDECI: Nonbond update at step 10125 UPDECI: Image update at step 10150 UPDECI: Nonbond update at step 10150 UPDECI: Nonbond update at step 10175 DYNA> 10200 176.40000-144823.64301 37351.85599-182175.49900 300.68321 DYNA PROP> 22.60872-144631.99779 37876.55518 191.64522 40855.54740 DYNA INTERN> 22256.74740 16069.90799 751.41457 4150.58637 377.17110 DYNA EXTERN> 12692.06399-167651.69454 .00000 .00000 .00000 DYNA IMAGES> 8641.81260 -79463.50849 .00000 .00000 .00000 DYNA PRESS> -4784.40708 -22452.62452 586.19037 340.73597 559644.93589 DYNA XTLE> -84669.21613 18.67894 60122.97467 1072.47737 ---------- --------- --------- --------- --------- --------- Crystal Parameters : Crystal Type = ORTH DYNA A = 74.24895 B = 103.08683 C = 73.11713 DYNA Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 DYNA PIXX = 88.91 PIYY = 592.37 PIZZ = 340.94 DYNA PIXY = 35.80 PIXZ = 36.38 PIYZ = 206.50 DYNA Gradient Norm = 146.73777 DYNAMC> Averages for the last 100 steps: AVER DYN: Step Time TOTEner TOTKe ENERgy TEMPerature AVER PROP: GRMS HFCTote HFCKe EHFCor VIRKe AVER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers AVER EXTERN: VDWaals ELEC HBONds ASP USER AVER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec AVER PRESS: VIRE VIRI PRESSE PRESSI VOLUme AVER XTLE: XTLTe SURFtension XTLPe XTLtemp ---------- --------- --------- --------- --------- --------- AVER> 100 176.40000-144813.57232 37269.33626-182082.90858 300.01893 AVER PROP> 22.57628-144648.54289 37768.10782 165.02943 36588.82188 AVER INTERN> 22302.04963 16100.09011 777.88335 4195.01031 374.72043 AVER EXTERN> 12445.24989-167343.46469 .00000 .00000 .00000 AVER IMAGES> 8636.99619 -79571.44380 .00000 .00000 .00000 AVER PRESS> 1132.37827 -25524.92619 -138.46699 -42.09613 560990.82077 AVER XTLE> -84697.72904 38.55309 60116.57172 425.56894 ---------- --------- --------- --------- --------- --------- Lattice Parameters> Averages for the last 100 steps: Crystal Parameters : Crystal Type = ORTH AVER A = 74.32133 B = 103.12211 C = 73.19653 AVER Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 AVER PIXX = -21.61 PIYY = -130.26 PIZZ = 25.58 AVER PIXY = 96.71 PIXZ = 74.35 PIYZ = 28.56 AVER Gradient Norm = 140.88757 DYNAMC> RMS fluctuations for the last 100 steps: FLUC> 100 176.40000 167.48173 109.68017 128.79175 .88293 FLUC PROP> .02698 166.80865 107.17796 24.55186 10192.35417 FLUC INTERN> 30.02593 61.56834 11.21059 22.41055 12.04859 FLUC EXTERN> 79.22112 153.29833 .00000 .00000 .00000 FLUC IMAGES> 84.62913 144.42726 .00000 .00000 .00000 FLUC PRESS> 7069.08291 1074.88973 863.85293 133.71316 511.20339 FLUC XTLE> 33.20445 54.82136 188.36358 340.10977 ---------- --------- --------- --------- --------- --------- Lattice Parameters> RMS fluctuations for the last 100 steps: Crystal Parameters : Crystal Type = ORTH FLUC A = .02779 B = .01122 C = .05726 FLUC Alpha = .00000 Beta = .00000 Gamma = .00000 FLUC PIXX = 186.46 PIYY = 209.21 PIZZ = 174.24 FLUC PIXY = 98.19 PIXZ = 116.72 PIYZ = 118.51 FLUC Gradient Norm = 53.00371 DYNAMC> Averages for the last 60200 steps: LAVE> 60200 176.40000-144728.64665 37267.46185-181996.10849 300.00384 LAVE PROP> 22.59724-144560.21114 37772.72569 168.43550 37763.83228 LAVE INTERN> 22309.64157 16135.45515 779.89314 4203.56001 375.80424 LAVE EXTERN> 14969.71456-188064.10406 .00000 .00000 .00000 LAVE IMAGES> 6246.92059 -58952.99368 .00000 .00000 .00000 LAVE PRESS> -9.73608 -25166.15211 1.36361 2.04991 562960.26670 LAVE XTLE> -113814.96926 1.75473 30912.88790 305.97306 ---------- --------- --------- --------- --------- --------- Lattice Parameters> Averages for the last 60200 steps: Crystal Parameters : Crystal Type = ORTH LAVE A = 73.98913 B = 103.30038 C = 73.65689 LAVE Alpha = 90.00000 Beta = 90.00000 Gamma = 90.00000 LAVE PIXX = -.21 PIYY = 1.11 PIZZ = 5.25 LAVE PIXY = 1.07 PIXZ = .55 PIYZ = -7.56 LAVE Gradient Norm = 156.68804 DYNAMC> RMS fluctuations for the last 60200 steps: LFLC> 60200 176.40000 336.96668 147.58231 301.80705 1.18804 LFLC PROP> .03798 334.92162 144.33102 34.22387 12125.44935 LFLC INTERN> 43.34323 71.47596 14.14906 41.66677 13.70322 LFLC EXTERN> 1819.24997 14529.29684 .00000 .00000 .00000 LFLC IMAGES> 1752.29334 14574.43613 .00000 .00000 .00000 LFLC PRESS> 8108.24872 1300.54741 988.40836 158.12481 3073.94746 LFLC XTLE> 16811.16578 88.49917 16985.72133 277.53923 ---------- --------- --------- --------- --------- --------- Lattice Parameters> RMS fluctuations for the last 60200 steps: Crystal Parameters : Crystal Type = ORTH LFLC A = .31258 B = .28494 C = .39795 LFLC Alpha = .00000 Beta = .00000 Gamma = .00000 LFLC PIXX = 220.35 PIYY = 225.06 PIZZ = 224.90 LFLC PIXY = 137.45 PIXZ = 138.34 PIYZ = 138.06 LFLC Gradient Norm = 71.14437 DRIFT/STEP (LAST-TOTAL): -.49688281 -9.94182564E-03 E AT STEP 0 : -144623.45 -144260.96 CORR. COEFFICIENT : -8.59850709E-02 -.51585640 UPDECI: Image update at step 10200 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 ***** LEVEL -3 WARNING FROM ***** ***** RESIDUE NUMBER OVERFLOW ****************************************** BOMLEV ( -5) IS NOT REACHED. WRNLEV IS 5 UPDECI: Nonbond update at step 10200 Execution terminated due to the detection of a fatal error. ABNORMAL TERMINATION MAXIMUM STACK SPACE USED IS 722336 STACK CURRENTLY IN USE IS 722336 MOST SEVERE WARNING WAS AT LEVEL -3 HEAP PRINTOUT- HEAP SIZE 10240000 SPACE CURRENTLY IN USE IS 14704504 MAXIMUM SPACE USED IS 20958104 FREE LIST PRINHP> ADDRESS: 1 LENGTH: 20016 NEXT: 6617145 PRINHP> ADDRESS: 6617145 LENGTH: 1770040 NEXT: 216312825 PRINHP> ADDRESS: 216312825 LENGTH: 4128 NEXT: 222572537 PRINHP> ADDRESS: 222572537 LENGTH: 360448 NEXT: 222934009 PRINHP> ADDRESS: 222934009 LENGTH: 360448 NEXT: 223295481 PRINHP> ADDRESS: 223295481 LENGTH: 360448 NEXT: 223660025 PRINHP> ADDRESS: 223660025 LENGTH: 6258688 NEXT: 0 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 19.01 HOURS CPU TIME: 39.37 HOURS ABNORMAL TERMINATION MAXIMUM STACK SPACE USED IS 722336 STACK CURRENTLY IN USE IS 722336 MOST SEVERE WARNING WAS AT LEVEL -3 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 19.01 HOURS CPU TIME: 40.45 HOURS ABNORMAL TERMINATION MAXIMUM STACK SPACE USED IS 722336 STACK CURRENTLY IN USE IS 722336 MOST SEVERE WARNING WAS AT LEVEL -3 $$$$$ JOB ACCOUNTING INFORMATION $$$$$ ELAPSED TIME: 19.01 HOURS CPU TIME: 40.63 HOURS --Boundary_(ID_cWuroSsyaf5c7h17f7bAbw)-- From chemistry-request@server.ccl.net Fri Jul 28 15:13:51 2000 Received: from yakko.cimav.edu.mx (root@[207.248.161.2]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id PAA32068 for ; Fri, 28 Jul 2000 15:13:47 -0400 Received: from glossman ([207.248.161.47]) by yakko.cimav.edu.mx (8.9.3/8.8.7) with SMTP id MAA02510 for ; Fri, 28 Jul 2000 12:22:43 -0600 Message-ID: <014401bff8cf$bbdced40$2fa1f8cf@cimav.edu.mx> From: "Dr. Daniel Glossman" To: "Computational Chemistry List" Subject: prediction of electrical and magnetic properties Date: Fri, 28 Jul 2000 13:09:27 -0700 MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: 8bit X-Priority: 3 X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook Express 5.00.2919.6600 X-MimeOLE: Produced By Microsoft MimeOLE V5.00.2919.6600 Dear netters: I am looking for references on the calculation and prediction of the electrical and magnetic properties of ceramics and crystals. (Journals, books, software, etc) Any help on how to start this search and to literature references will be appreciated. Thanks in advance. Dr. Daniel Glossman Mitnik **************************************************************************** ******** Dr. Daniel Glossman Mitnik Centro de Investigación en Materiales Avanzados (CIMAV) Departamento de Polímeros Miguel de Cervantes 120 Complejo Industrial Chihuahua Chihuahua, Chih. 31109 Mexico Phone: (52) 14 391151 FAX: (52) 14 391112 E-mail: glossman@mail.cimav.edu.mx glossman@hotmail.com **************************************************************************** ******** From chemistry-request@server.ccl.net Fri Jul 28 14:25:21 2000 Received: from ne059.cm.utexas.edu (ne059.cm.utexas.edu [146.6.145.59]) by server.ccl.net (8.8.7/8.8.7) with SMTP id OAA31822 for ; Fri, 28 Jul 2000 14:25:21 -0400 Received: from ne057.cm.utexas.edu by ne059.cm.utexas.edu (AIX 3.2/UCB 5.64/4.03) id AA10818; Fri, 28 Jul 2000 13:20:28 -0500 Message-Id: <3981EB26.6F70A956@eeyore.cm.utexas.edu> Date: Fri, 28 Jul 2000 13:20:54 -0700 From: "Isaac B. Bersuker" X-Mailer: Mozilla 4.7 [en] (WinNT; I) X-Accept-Language: en,zh,zh-CN,zh-TW Mime-Version: 1.0 To: Per-Ola Norrby Cc: chemistry@ccl.net Subject: Re: CCL:TM force fields References: <397C5C3F.28DEEEDA@eeyore.cm.utexas.edu> Content-Type: text/plain; charset=koi8-r Content-Transfer-Encoding: 7bit Dear Dr. Norrby: Instead of getting iritated and offended, you better respond to the specific criticism of the force field idea in application to TM systems. This is SCIENCE, let me remind you, and the main condition of its progress is open discussion and proof of statements. I proved my statements in the references I gave earlier (that you deleted) and I would expect you to show that my proof is wrong. Just stating that one made calculations with good results does not prove anything, with arbitrary parameters (changed from one compound to another) everybody can get any a priori desired results. And, please, don't reffer to "authorities". I respect them all and their point of view, but the scientific truth is more important. Regards Isaac Per-Ola Norrby wrote: > Isaac B. Bersuker wrote: > > >I repeat my firm conviction that, in general, there are > >no force fields for transitiom metal systems (see my latest book ... > > (The rest of the message deleted). > > I've seen this comment a couple of times now, and I'm getting > irritated. This is a very sweeping statement, and insulting to those > who have produced good work in this area. It is only true if you > interprete it like "it is not possible to achieve infinite accuracy > for all possible TM complexes", but stated like that it would be > equally true of any method. For specific classes of complexes, it is > possible to get high accuracy with force field methods. It's just a > question of having a flexible enough force field and doing a careful > parameterization. Check out the book by Comba and Hambley, > "Molecular Modeling of Inorganic Compounds", a new edition is comming > out soon. We also have a review in press in Coord.Chem.Rev. on how > to do this parameterization (don't know when it's going to appear). > For some classical reviews, see: > > C.R. Landis, D.M. Root, T. Cleveland, in: K.B. Lipkowitz and D.B. > Boyd (Eds.), Reviews in Computational Chemistry, Vol. 6, VCH > Publishers, Inc., New York, 1995, p. 73-148. > > M. Zimmer, Chem. Rev. 95 (1995) 2629. > > P. Comba, Comments Inorg. Chem. 16 (1994) 133. > > B.P. Hay, Coordination Chemistry Reviews 126 (1993) 177. > > (Yes, I know, I left several out, this is just a selection based on > personal preference). > > The general force fields are also advancing. You can still > get whooping errors, and should validate carefully, but I've actually > been surprised several times by the results you can get without > specific parameterization. I'd like to point to UFF (not all > implementations though :-), VALBOND (not a complete force field, but > a very interesting addition to UFF), and the force fields in PCModel > and Spartan. There are others, but I don't have personal experience > with them. > > Per-Ola > -- > > ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ > * Per-Ola Norrby, Associate Professor > * The Royal Danish School of Pharmacy, Dept. of Med. Chem. > * Universitetsparken 2, DK 2100 Copenhagen, Denmark > * Tel. +45-35306506, fax +45-35306040 > * Email: peo@dfh.dk (preferred), peo@compchem.dfh.dk > * WWW: http://compchem.dfh.dk/PeO/ > > -= This is automatically added to each message by mailing script =- > CHEMISTRY@ccl.net -- To Everybody | CHEMISTRY-REQUEST@ccl.net -- To Admins > MAILSERV@ccl.net -- HELP CHEMISTRY or HELP SEARCH > CHEMISTRY-SEARCH@ccl.net -- archive search | Gopher: gopher.ccl.net 70 > Ftp: ftp.ccl.net | WWW: http://www.ccl.net/chemistry/ | Jan: jkl@ccl.net -- Isaac B. Bersuker Institute for Theoretical Chemistry Department of Chemistry & Biochemistry The University of Texas at Austin Austin, TX 78712, USA Ph: (512) 471-4671 Fax: (512) 471-8696 Email: bersuker@eeyore.cm.utexas.edu From chemistry-request@server.ccl.net Fri Jul 28 16:01:39 2000 Received: from copland.udel.edu (copland.udel.edu [128.175.13.92]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id QAA32442 for ; Fri, 28 Jul 2000 16:01:39 -0400 Received: from localhost (gijukt@localhost) by copland.udel.edu (8.9.3/8.9.3) with ESMTP id QAA24999 for ; Fri, 28 Jul 2000 16:01:38 -0400 (EDT) Date: Fri, 28 Jul 2000 16:01:38 -0400 (EDT) From: Giju Thomas Kalathingal To: chemistry@ccl.net Subject: Help on Basis II trouble Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hi everybody, I have done a set of calculations on transition metal complexes with a series of basis sets at B3LYP level using Gaussian98. These included CEP, SDD, LANL2DZ (as avaialable with g98) and basis II as discribed in 'Reviews in Computational Chemistry', Vol. 8, K.B. Lipkowitz and D.B. Boyd (Eds), VCH, New York, p. 63 - 144 (1996). For basis II, I have used Hay&Wadt pseudo-ECP and the corresponding valence basis sets for transition metal. For main group elements, 6-31G(d,p) was used. The problem is that, of all the basis sets I used, the basis II gives an imaginary frequency. Now I am worried about the time I spent and the already published results using this basis sets by other people. Here is the question. Does the mixing of ECP and all electron basis sets in basis II make the selection incompatible? More specifically, is the mixing in basis II is compatible? Or, basis II is correct while all others (CEP, SDD, LANL2DZ) are wrong? Hope you are able to help me. Thanks, Giju From chemistry-request@server.ccl.net Fri Jul 28 17:04:06 2000 Received: from relay1.scripps.edu (relay1.scripps.edu [137.131.200.29]) by server.ccl.net (8.8.7/8.8.7) with ESMTP id RAA32765 for ; Fri, 28 Jul 2000 17:04:05 -0400 Received: from chagall.scripps.edu (chagall.scripps.edu [137.131.252.60]) by relay1.scripps.edu (8.9.3/TSRI-3.2.1r) with ESMTP id OAA16031; Fri, 28 Jul 2000 14:02:03 -0700 (PDT) Received: from localhost (salsb@localhost) by chagall.scripps.edu (8.9.2/TSRI-3.0) with SMTP id OAA399551; Fri, 28 Jul 2000 14:02:03 -0700 (PDT) Date: Fri, 28 Jul 2000 14:02:02 -0700 (PDT) From: Fred Salsbury X-Sender: salsb@chagall To: Joe Huang cc: charmm-bbs@csir.org, chemistry@ccl.net Subject: Re: CCL:Error message in CHARMM: RESIDUE NUMBER OVERFLOW! In-Reply-To: <3981C56B.5F58B41F@uh.edu> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII Hello -- First, I wouldn't consider changing imgfrq to be a satisfactory solution to this problem. Actually, it's not clear to me why that would work. I've gotten this problem myself. What it is is that maxres (which is real residues plus image) is 32000 even for the large and xlarge version of charmm. The solution to this problem was to recomplie charmm, but with changing the maxres from 32000 to something bigger, say 60000. This is in dimens.fcm. But without changing the heap or stack sizes. If the extra residues are water molecules then the standard stack and heap sizes should be able to handle much more than 32000 residues. Of course you will still blow out the resid field as the limit there is 9999 , but that just means you can't sele by resid for those water molecules. A less satisfactory change might be to reduce cutim, as that will reduce the number of image resiudes. I've run on some big systems and I've found that the stack/heap sized only became a problem once with ewald and the charge grid there and I found that could be avoided just by reducing slightly the FFT dimensons. Hope this helps Fred On Fri, 28 Jul 2000, Joe Huang wrote: > Hi, dear computational chemist: > I have a very big system (~60K atoms) running MD with CHARMM(c26b1) and > this is the second time I encounter this kind of error message. When I > got this error message long time ago, some people suggested me to > recompile a bigger CHARMM version and(or) reduce the frequency for > IMGFRQ; I did recompile a bigger CHARMM version (2 times the size of > large version) and the MD simulation could be continued afterward. But, > now, after 60000 steps of simulations in production phase (2 fs timestep > with SHAKE), I encounter this error message again! > This time, I don't think I should recompile CHARMM because I must > allocate more swap spaces or add more physical memories for bigger > CHARMM to run in our Linux Beowulf cluster (from last time's > experience). I do need to find the real problem. The error message > (last part of the output file) is attached. Can anybody give me some > help for this problem. Thanks!!! > > > Joe > http://adrik.bchs.uh.edu/~jhuang >