From chemistry-request@ccl.net Mon Nov 3 06:27:41 2003 Received: from mail.uvigo.es (mail.uvigo.es [193.146.32.91]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA3BR8hP008339 for >ccl.net>; Mon, 3 Nov 2003 06:27:09 -0500 Received: from mail.uvigo.es (localhost [127.0.0.1]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id hA3BR7ck009117 for >ccl.net>; Mon, 3 Nov 2003 12:27:07 +0100 Received: from correo.uvigo.es (correo.uvigo.es [193.146.32.68]) by mail.uvigo.es (8.12.9/8.12.1) with ESMTP id hA3BR6uA009103 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for >ccl.net>; Mon, 3 Nov 2003 12:27:06 +0100 Received: from correo (correo [193.146.32.68]) by correo.uvigo.es (8.12.9/8.12.5) with ESMTP id hA3BR6Qk017438 for >ccl.net>; Mon, 3 Nov 2003 12:27:06 +0100 Date: Mon, 3 Nov 2003 12:27:06 +0100 (CET) From: Carlos Silva Lopez >uvigo.es> X-X-Sender: To: >ccl.net> Subject: Fractional Occupation Numbers 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 hA3BRfhP008360 Hello CCLers Thanks for these first suggestions, I think I should clarify my question since it seems it has led to some misunderstandings. I came across with a few papers from Goddard and Orlova such as: JChemPhys v111 n17 p7705 1999 JChemPhys v112 n23 p10085 2000 They use g98 and several functionals with partial occupation numbers to study concerted reactions and they report really nice results compared with MCSCF methods. I would like to use this approach but I don not find any documentation for g98. Someone suggested to try a fractional total charge for the system, this is not what I ment to do. Furthermore, gaussian will crash because the code is expecting an integer for that value, not a floating point. Thanks for your feedback _-_-_-_-_-_-_-_-_-_-_-_- Carlos Silva Lspez Dept. Qummica Organica Universidade de Vigo Phone:0034 986812226 -_-_-_-_-_-_-_-_-_-_-_-_ From chemistry-request@ccl.net Mon Nov 3 04:04:28 2003 Received: from ozone.cs.vu.nl (ozone.cs.vu.nl [130.37.24.158]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA393thP032053 for ; Mon, 3 Nov 2003 04:03:56 -0500 Received: from chem.vu.nl (far27.chem.vu.nl [130.37.148.106]) by ozone.cs.vu.nl with esmtp (Smail #87) id m1AGacn-000NHbC; Mon, 3 Nov 2003 10:03 +0100 Message-ID: <3FA6047B.4070200(at)chem.vu.nl> Date: Mon, 03 Nov 2003 08:32:11 +0100 From: Anton Feenstra Organization: Vrije Universiteit Amsterdam - Pharmaceutical Chemistry User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.0; en-US; rv:1.4.1) Gecko/20031008 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry(at)ccl.net Subject: Re: CCL:Linux Cluster References: <3FA0CEC5.8010502(at)silex.dk> <1510089009.20031031094924(at)bancorp.ru> <3FA2258B.1010809(at)silex.dk> In-Reply-To: <3FA2258B.1010809(at)silex.dk> Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=-2.6 required=7.0 tests=EMAIL_ATTRIBUTION,IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES, REPLY_WITH_QUOTES,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) Kenneth Geisshirt wrote: > Gregory Shamov wrote: > >> KG> A number of companies build clusters (e.g., the one I work for), >> KG> and you can buy cluster distributions like MandrakeSoft's >> KG> Clustering product. Finally, you can build a cluster by hand (ok >> KG> if the number of nodes is less than 6). >> >> And what happens if the number of nodes becomes 7 ? Or even 8 ? > > > My point is that building a cluster by hand does not scale well. If you > plan a large cluster (32+ nodes) you will need some kind of automated > tool. If you build a 4-node cluster and add a new node (different > hardware e.g., an old office pc) you can do it by hand. Im my experience, if you keep the hardware relatively homogeneous (i.e. at least 16 nodes at a time are identical, and no more than say 2-3 different types of nodes) any number of nodes is as much work as only one. It isn't too difficult to set up a system with net-boot and harddisk images that installs new nodes automatically, and re- installs nodes in case of crashes or other problems. I've done this now for two different 'off-the-shelf' clusters and after initial tweaking of setups (mostly related to network-card and boot-rom specifics) everything is rock-stable and nearly self maintaining... I've never done anything similar with e.g. 'old' office PC's (i.e. in-homogeneous hardware), but it probably is more work than it is worth relative to the average low speed of the 'old' CPU's. -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam | |( | )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610 | | | Feenstra(at)chem.vu.nl - www.chem.vu.nl/~feenstra/ | | | "If You See Me Getting High, Knock Me Down" | | | (Red Hot Chili Peppers) | |_____________|_______________________________________________________| From chemistry-request@ccl.net Mon Nov 3 09:43:12 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 hA3EgfhP018864 for ; Mon, 3 Nov 2003 09:42:41 -0500 Received: from smeagol.unb.ca (smeagol.unb.ca [131.202.3.52]) by mailserv.unb.ca (8.12.10/8.12.6) with ESMTP id hA3EgYmc019812; Mon, 3 Nov 2003 10:42:34 -0400 Received: from smeagol.unb.ca (localhost.localdomain [127.0.0.1]) by smeagol.unb.ca (8.12.8/8.12.8) with ESMTP id hA3EgYvQ005791; Mon, 3 Nov 2003 10:42:34 -0400 Received: (from apache@localhost) by smeagol.unb.ca (8.12.8/8.12.8/Submit) id hA3EgXnJ005788; Mon, 3 Nov 2003 10:42:33 -0400 Received: from raven.chem.unb.ca (raven.chem.unb.ca [131.202.164.46]) by webmail.unb.ca (IMP) with HTTP for ; Mon, 3 Nov 2003 10:42:33 -0400 Message-ID: <1067870553.3fa669593a9a1$at$webmail.unb.ca> Date: Mon, 3 Nov 2003 10:42:33 -0400 From: "Flight, Robert Maxwell" Reply-to: robert.flight$at$unb.ca To: Alex Sutcliffe , @unb.ca, Computational Chemistry List Subject: Re: ADL: fixing non-integral charges References: <20031103143214.GA21755@alex> In-Reply-To: <20031103143214.GA21755@alex> 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: 131.202.164.46 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=-2.4, required 5, FROM_HAS_MIXED_NUMS, IN_REP_TO, QUOTED_EMAIL_TEXT, REFERENCES, SPAM_PHRASE_00_01, USER_AGENT, USER_AGENT_IMP) X-Spam-Status: No, hits=-2.3 required=7.0 tests=IN_REP_TO,QUOTED_EMAIL_TEXT,REFERENCES,REPLY_WITH_QUOTES, USER_AGENT_IMP version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Hi Alex, > I am trying to use autodock via adt. When I read in my ligand it > complains that the charge on the molecule is not integral and to fix > this in the written file and mentions specific residues. From the > written pdbq file an example is > > ATOM 1 N ALA A 295 76.602 58.846 18.320 1.00 15.64 -0.520 > ATOM 2 HN1 ALA A 295 76.335 59.392 19.139 1.00 0.00 0.000 > ATOM 3 HN2 ALA A 295 76.036 59.070 17.502 1.00 0.00 0.000 > ATOM 4 HN3 ALA A 295 77.509 59.124 17.946 1.00 0.00 0.000 > ATOM 5 CA ALA A 295 76.552 57.441 18.657 1.00 15.00 0.215 > ATOM 6 C ALA A 295 76.956 56.616 17.418 1.00 18.88 0.526 > ATOM 7 O ALA A 295 77.711 55.640 17.578 1.00 17.66 -0.500 > ATOM 8 CB ALA A 295 75.172 57.039 19.105 1.00 12.54 0.031 > From what you show here, I'm guessing that the alanine is at a break point in the protein (if it was continuous then the Nitrogen should have only one H like the other one you listed), you should visually check this to be sure. I have personally had a lot of trouble with partial charges on any residues that are at a break in my proteins. > ie it only has HN not HN1,2,3 and the charge on it is .248 thus giving a > net charge of 0. > > So to fix this file do I want to simply delete the extra HN lines and > change the charge from 0 to 0.248 or do I fix it some other way? Personally, I have started ignoring the message as long as residue was not near or part of the active site, and I have not noticed it making any difference in my docking results. If you really wanted, you could distribute a positive 0.248 charge evenly between the three hydrogens. That would be the safe bet, and is relatively painless if you only have to do it once. Hope this helps. Cheers, -Robert *************************** Robert Flight Master Candidate Computational Chemistry Department of Chemistry University of New Brunswick Fredericton NB, Canada E3B 6E2 e-mail: robert.flight$at$unb.ca *************************** "A computer terminal is not some clunky old television with a typewriter in front of it. It is an interface where the mind and body can connect with the universe and move bits of it about." -- Hitch Hikers Guide to the Galaxy From chemistry-request@ccl.net Mon Nov 3 10:32:07 2003 Received: from xmail2.wiley.com (xmail2.wiley.com [208.215.179.22]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA3FVYhP021200 for ; Mon, 3 Nov 2003 10:31:35 -0500 Received: from wtest.wiley.com ([10.4.200.37]) by xmail2.wiley.com (8.12.10/8.12.10) with ESMTP id hA3Fd42w012418 for ; Mon, 3 Nov 2003 10:39:04 -0500 (EST) Subject: new North American Editor -- JCC To: chemistry$at$ccl.net X-Mailer: Lotus Notes Release 5.0.7 March 21, 2001 Message-ID: From: JGlover$at$wiley.com Date: Mon, 3 Nov 2003 10:32:57 -0500 X-MIMETrack: Serialize by Router on wtest/IT/Wiley(Release 5.0.10 |March 22, 2002) at 11/03/2003 10:30:19 AM MIME-Version: 1.0 Content-type: text/plain; charset=iso-8859-1 X-Spam-Status: No, hits=0.8 required=7.0 tests=NO_REAL_NAME version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Content-Transfer-Encoding: 8bit X-MIME-Autoconverted: from quoted-printable to 8bit by server.ccl.net id hA3FW7hP021231 New Editor Announcement: John Wiley & Sons wishes to acknowledge Dr. William Jorgensen for his work as North American Editor of the Journal of Computational Chemistry over the past 2 years. Thanks to Dr. Jorgensen's efforts, the journal has experienced a period of growth and progress, especially in the area of life sciences. Dr. Jorgensen has accepted, effective January 2004, an opportunity with the American Chemical Society as Editor of the Journal of Chemical Information and Computer Sciences, as well as a new journal to be annnounced in 2004. We thank Dr. Jorgensen for his services and wish him the best of luck. As Dr. Jorgensen steps down, we are pleased to announce the appointment of Dr. Charles L. Brooks, III as the new North American Editor of the Journal of Computational Chemistry beginning January 2004. Dr. Brooks leads a research group at the Scripps Research Institute in La Jolla, California whose focus is computational biophysics and chemistry. He is also a member of the National Biomedical Computation Resource Advisory Committee; an NSF reviewer for proposals in chemistry, chemical instrumentation biological instrumentation, and biophysics; and the initiator and organizer of the La Jolla Interfaces in Science Interdisciplinary Training Program. Dr. Brooks' reputation as one of the foremost scientists in the field of molecular biology is well-known; he is a dedicated scientist with an impressive background and we are pleased and excited that he has accepted this editorship with JCC. We would also like to acknowledge Drs. Gernot Frenking and Hiroshi Nakatsuji for their continuing editorial efforts; they will of course remain as Editors for Europe, Asia, and the Far East. From chemistry-request@ccl.net Mon Nov 3 18:16:21 2003 Received: from sentry.ucr.edu (sentry.ucr.edu [138.23.226.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA3NFmhP010114 for ; Mon, 3 Nov 2003 18:15:49 -0500 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentry.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id ATA18367; Mon, 3 Nov 2003 15:15:47 -0800 (PST) Reply-To: From: "Donald Keidel" To: , "Donald Keidel" Subject: CCL: Summary of Program to search SD/MDL formatted files from chemical companies Date: Mon, 3 Nov 2003 15:15:43 -0800 Organization: UCR Message-ID: <000001c3a260$67f86cc0$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 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) Thank you all for all your responses and all your help. I greatly appreciate everything. Have a great day. Don Don, The chemoinformatics toolkit CACTVS has very powerful substructure search capabilities. It is free for academic use. See http://www2.ccc.uni-erlangen.de/software/cactvs/. We have, e.g., based our online Enhanced NCI Database Browser (http://cactus.nci.nih.gov/ncidb2/) on it. We are using CACTVS to search in SD files numbering in the millions of compounds (although you get a huge additional speedup if you first convert them into the internal CACTVS format). We are working to put a more complete CACTVS documentation together - if you are interested, feel free to contact me. For all other questions, please contact the author of CACTVS, Wolf-Dietrich Ihlenfeldt (wdi|at|xemistry.com). Cheers, Marc Don, If you need a chemically intelligent database solution that can also be used to build an intra- or internet application, please check out JChem Base. http://www.chemaxon.com/products.html#JChemBase You can try it here: http://www.jchem.com/examples.html JChem can be downloaded from the site. An example application that can be easily customized is included in the package. The software is in Java so it is portable. It can be connected to several databases, like MySQL, PosgreSQL, Oracle, etc. Best regards, Ferenc If you look for a free substructure search program, try obgrep which is a tool available at the open babel sourceforge web site http://sourceforge.net/projects/openbabel/ The program uses daylight SMART chemical language to perform the query (http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) Unfortunately, the program is not in the current release (1.100.1) for the moment, but you can get it by anonymous access to the CVS repository. Regards, Fabien Hi, the Omega from Openeyes (http://www.eyesopen.com) might do what you ask looking for, and is free for academics, as far as I know. Th Don, The CACTVS Chemoinformatics toolkit, which contains a full and competitive substructure search engine, is free for academic use and can be downloaded from www.xemistry.com/academic. This engine drives the NCI database (http://cactus.nci.nih.gov/ncidb2). This is not a graphical environment, but a script tool (but because of this far more powerful than ISIS/Base - it reads ISIS query files and Daylighgt SMARTS, though) Don, not sure what exactly you mean by "to search SD/MDL formatted files". Our open source java library for structural chemo- and bioinformatics, The Chemistry Development Kit (CDK) [1] can read SD/MDL files and perform a number of operations on it, like searching for a particular substructure, etc. Other operations, like calculating certain descriptors, can be quickly implemented. The CDK lives on http://cdk.sourceforge.net. Feel free to contact the CDK development team on the cdk-devel|at|lists.sourceforge.net mailing list to discuss whatever CDK-related question you have. Cheers, Chris Hi, Don, CACTVS is a freely available chemical extension of the Tcl scripting language [http://www2.ccc.uni-erlangen.de/software/cactvs/]. There are some commands to allow you to search chemical database files (either within a flat file or from a DBMS). Although a powerful language, the main drawback is the lack of documentation. Consequently, I am attaching a PDF of the beginning of a manual I was trying to create from notes of some of our group members here. I warn you that it is incomplete (and on hold indefinitely, as priorities have shifted) and may not be totally accurate from a conceptual viewpoint. However, that said, something is better than nothing so... Also, towards the end of the manual I have just added the structure searching notes verbatim. Hope the information helps, Karen Hi Donald, MarvinView can search SD files Hope this helps Best regards J.C. From chemistry-request@ccl.net Mon Nov 3 15:58:47 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 hA3KwFhP002856 for ; Mon, 3 Nov 2003 15:58:16 -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 hA3Kw8R9005496; Mon, 3 Nov 2003 15:58:14 -0500 (EST) Message-ID: <009901c3a24d$193f0d90$88541a42@bobcat> From: "Robert Duke" To: "Jim Phillips" , References: Subject: Re: CCL:PMEMD 3.1 Release - High Scalability Update to PMEMD Date: Mon, 3 Nov 2003 15:57:27 -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=-1.5 required=7.0 tests=ORIGINAL_MESSAGE,QUOTED_EMAIL_TEXT,REFERENCES version=2.55 X-Spam-Checker-Version: SpamAssassin 2.55 (1.174.2.19-2003-05-19-exp) Jim - It was not my goal to be unfair in the comparisons, but to make the comparisons that I could, given the available benchmarks. I very specifically said something to the effect of the 90K atom benchmarks being "apples and oranges", but that I was assuming that the NAMD team would have picked a 90K atom benchmark representative of 90K atom production runs of NAMD. To my mind, the choice of a 12 A cutoff is unfortunate, in that it consumes more time in direct force calcs than is typically necessary for a PME simulation; we more typically see folks use 8 to 9 A values, and all the previously published PMEMD benchmarks indeed do use 8 A cutoffs. Note however, that the 3-fold difference is not strictly correct; the direct force computation typically scales well, whereas this is not so true of the 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 (;-}). I presumed you all were actually using the larger cutoff to compensate for errors associated with the use of a multi-timestep approach 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 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 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). 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 mostly used 4 processors per node, but specify total cpu's and nodes below so you can distinguish (for folks unfamiliar with the alphaservers, or sp4's for that matter, you can sometimes improve performance by not using all the cpu's associated with a node, which is basically a clump of cpu's with some shared components). Results are in seconds for 1000 steps. 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 Now, there is a published NAMD 2.5b2 benchmark on the SGI Origin that shows 2.5b2 outperforming 2.4 by 24% at 1 proc, tarpering down to 10% at 64 procs and 0% at 126 procs (and doing worse at 252 procs). So taking that into account, PMEMD 3.1 is probably roughly 50% faster at the low end, and exceeds the NAMD max throughput slightly using about half the processors required by NAMD. By the way, I dislike this specific benchmark because 1) it is a small system, which means performance is less critical and you will also hit top end performance at a lower processor count, 2) it is a constant volume simulation; at least for us our longer runs are constant pressure and constant pressure is harder to scale, 3) it really does almost no i/o, which is unrealistic; reasonable amounts of i/o will impact high end scaling slightly, and 4) if I am concerned about performance, I use 8 A cutoffs unless it is clear that a larger cutoff is needed. On the less competitive, side, I have looked at what you all have done on scaling, and am impressed, and would be even more impressed with decent scaling on the larger systems in conjunction with more reasonable cutoffs. I would expect the NAMD effort to be difficult to keep up with. My goal is to provide decent scaling to the Amber community, as a one man effort. My apologies to the CCL list for the long mail. Regards - Bob Duke ----- Original Message ----- From: "Jim Phillips" To: Sent: Friday, October 31, 2003 3:29 PM Subject: CCL:PMEMD 3.1 Release - High Scalability Update to PMEMD > Dear CCL, > > Since this message and particularly the PMEMD 3.1 update notes (available > at http://amber.scripps.edu/pmemd.3.1.UpdateNote.html) spend considerable > time on comparisons to NAMD, I feel that a couple of clarifications are in > order regarding NAMD performance and benchmarking. > > My first point is that not all 90K atom simulations are comparable. The > bulk of the computation is in the direct nonbonded interactions, which > scale roughly as cutoff^3 * numatoms^2 / volume. The apoa1 NAMD benchmark > uses a 12A cutoff, the default specified by the CHARMM force field. I can > not find any indication of the cutoff distance of the Factor IX benchmark > used by PMEMD, but the Amber 7 manual uses an 8A cutoff by default. This > difference alone indicates that *NAMD is doing three times more work* than > PMEMD, which is hardly fair. > > An independent comparison of CHARMM, AMBER, and NAMD running the same > Joint Amber-Charmm (JAC) 9A cutoff with PME benchmark is available at > http://www.scripps.edu/brooks/Benchmarks/ and demonstrates that NAMD 2.4 > serial performance is similar to other programs, with some differences > depending on platform. Note that NAMD 2.4 is 18 months old and last > month's NAMD 2.5 has been observed by users to be up to 40% faster on some > platforms, as well as incorporating the scalability advances reported in > our SC2002 paper (http://www.sc-2002.org/paperpdfs/pap.pap277.pdf), which > received a Gordon Bell Award. > > NAMD has historically been tuned for HP Alpha and AMD Athlon, with major > improvements in 2.5 for Intel IA64 and IA32. NAMD currently runs twice as > fast on Itanium 2 as it does on POWER4. Our local users have never used > an IBM SP for production, and while NCSA recently acquired several p690s, > these were purchased for large shared memory applications and are not cost > effective for NAMD simulations (vs our $30K 48-CPU Athlon clusters). > > Most recent NAMD scalability tuning has been done on PSC's Lemieux, and > very little on any IBM SP. There are also serious performance issues with > the interaction between the Charm++ (http://charm.cs.uiuc.edu) > communication layer used in NAMD and IBM's MPI implementation in which > MPI_Isend fails to send data until the next MPI call after the received > node has called MPI_Iprobe and posted an MPI_Recv. Charm++ relies on this > idiom to implement message driven execution top of MPI, and it works > acceptably on other platforms. We are working to address this issue. > > In conclusion, NAMD is available free of charge as source code or binaries > for a dozen platforms and reads CHARMM and AMBER input file formats, so > it is relatively painless to run your own benchmarks to decide if NAMD > provides a performance benefit for your simulations. > > Sincerely, > > James Phillips, Ph.D. > Senior Research Programmer for NAMD Development > http://www.ks.uiuc.edu/Research/namd/ > > > On Fri, 31 Oct 2003, Robert Duke wrote: > > > We are proud to announce the release of version 3.1 (the first major > > performance update) of PMEMD (Particle Mesh Ewald Molecular Dynamics). > > > > PMEMD is a new version of the Amber module "Sander", and has been written > > with the major goal of improving performance in Particle Mesh Ewald > > molecular dynamics simulations and minimizations. The code has been totally > > rewritten in Fortran 90, and is capable of running in either an Amber 6 or > > Amber 7 mode. Functionality is more complete in Amber 6 mode, with the > > Amber 7 mode designed mostly to do the same sorts of things that Amber 6 > > does, but with output that is comparable to Amber 7 Sander. The calculations > > done in PMEMD are intended to replicate either Sander 6 or Sander 7 > > calculations within the limits of roundoff errors. The calculations are just > > done more rapidly in about half the memory, and runs may be made efficiently > > on significantly larger numbers of processors. > > > > The primary site for high scalability work on PMEMD 3.1 has been the > > Edinburgh Parallel Computing Centre (IBM P690 Regatta, 1.3 GHz Power4 CPU's, > > 1280 total processors), and we would like to thank EPCC for making their > > facilities available for this work. At EPCC, we have obtained maximum > > throughputs of 3.65 nsec/day (constant volume, 320 processors) and 3.48 > > nsec/day (constant pressure, 320 processors) for a 90906 atom PME solvated > > protein simulation. This compares to 0.41 nsec/day (constant pressure, 128 > > processors) for Sander 7 on the same simulation problem and 3.43 nsec/day > > (1024 processors) for NAMD on a similar simulation problem (92,224 atoms). > > More significant is performance at the "50% scalability point", the point > > where adding more processors will decrease compute efficiency below 50%. > > PMEMD 3.1 runs the above simulation with at least 50% scalability on 128 > > processors, producing 2.85 nsec/day throughput. For Sander 7, only 16 > > processors may be used without going below 50% scalability, and throughput > > is 0.28 nsec/day. For NAMD, 256 processors may be used at 50% scalability, > > but throughput is only 1.3 nsec/day. Additional benchmark data is > > presented in the Update Note available at the Amber website. > > > > PMEMD was developed by Dr. Robert Duke in Prof. Lee Pedersen's Lab at > > UNC-Chapel Hill, starting from the version of Sander in Amber 6. Funding > > support was provided by NIH grant HL-06350 (PPG) and NSF grant 2001-0759-02 > > (ITR/AP). When citing PMEMD (Particle Mesh Ewald Molecular Dynamics) in the > > literature, please use both the Amber Version 7 citation given in the Amber > > 7 manual, and the following citation: > > > > Robert E. Duke and Lee G. Pedersen (2003) PMEMD 3.1, University of North > > Carolina-Chapel Hill > > > > PMEMD is available without charge to users who have an existing license for > > Amber (version 6 or 7). For more information, and to download the code, > > please go to: > > > > http://amber.scripps.edu/pmemd-get.html > > > > > > - Robert Duke (UNC-Chapel Hill) and David Case (The Scripps Research > > Institute) > > > > > > > > > > > > Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST|at|ccl.net > > HOME Page: http://www.ccl.net | Jobs Page: http://www.ccl.net/jobs > > > > > > > > > > > > > > > > > > > > > -= 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 Mon Nov 3 18:23:37 2003 Received: from sentry.ucr.edu (sentry.ucr.edu [138.23.226.224]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id hA3NN5hP010527 for ; Mon, 3 Nov 2003 18:23:05 -0500 Received: from dopetec (dunn4470.ucr.edu [138.23.156.82]) by sentry.ucr.edu (Mirapoint Messaging Server MOS 3.2.1-GA) with ESMTP id ATA18660 for ; Mon, 3 Nov 2003 15:23:04 -0800 (PST) Reply-To: From: "Donald Keidel" To: Subject: CCL:Summary of Searchable Chemical Database - Substructures and Similarity Date: Mon, 3 Nov 2003 15:22:57 -0800 Organization: UCR Message-ID: <000001c3a261$6a162730$529c178a@dopetec> MIME-Version: 1.0 Content-Type: text/plain; charset="iso-8859-1" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.3416 Importance: Normal X-MimeOLE: Produced By Microsoft MimeOLE V6.00.2800.1165 X-Spam-Status: No, hits=-0.5 required=7.0 tests=QUOTED_EMAIL_TEXT 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 hA3NNbhP010561 Thank you all for all responses and all help. These comments have been a great help. Have a great day. Don Dear Donald, I have read your inquiry on CCL.NET. You should have a look at our C@ROL system (http://www.mol-net.de/software/carol/index.html) since C@ROL offers 3D pharmacophore searches, substructure searches, similarity searches, and innovative transformation searches in its chemical databases. Please, check also http://www.mol-net.de/software/carol/carol_moreinfo.html in order to download additional information material. On http://www.mol-net.de/software/carol/carol_demo.html you may have free access to the demo version of C@ROL. Please, contact me for further questions. Best regards, Matthias Pfvrtner Hi Don, > > Try ChemNavigator at www.chemnavigator.com (you have to register). > > You'll get access to more than 12 million chemical samples, a search > interface, and all info to order compounds. > Another commercial (free demo accounts) alternative which is somewhat complementary to CAS is http://infochem.de SPRESIweb has 4.5 million organic and organo-metallic compounds, searchable by structure, substructure and reaction; 3.5 million reactions abstracted from 380000 references (including 98000 patents). Donald, ChemNavigator has an evaluation for access to their large database. See their website. Another large one is MDL s screening collection database. Otherwise, I recommend a slower step of just contacting vendors and getting their catalogs in SDF format shipped (freely available) to you regularly. --Ajit I think Asinex has a similar collection... Doug H Douglas Henry I suggest that you contact Tripos. Tripos has developed a number of software products, e.g. UNITY, for mining data bases. Donald, Did you try the NCI database (cactvs.nci.nih.gov) ? Dear Mr. Keidel, we received your request in chemystry_at_ccl.net according a "Searchable Chemical Database". Have you already heard about SPRESIweb? In case not, we would like to introduce you SPRESIweb: SPRESIweb is a structure and reaction database containing 4.5 million organic and organometallic compounds and 3.5 million reactions abstracted from 380,000 references and 98,000 patents covering the chemical literature published since 1974. Therefor SPRESIweb is one of the largest structure and reaction databases worldwide. SPRESIweb includes also comprehensive additional factual data on chemical, physical and biological properties of the compounds as well as textual information like keywords and conditions described in the references. The search can be carried out for molecules, reactions and references. SPRESIweb offers a lot of different links to external sources like several document delivery services (such as FIZ AutoDoc, CISTI and soon subito), patent offices (Espacenet, US Patent & Trademark Office and MicroPatent)and ChemNavigator. Unfortunately we don't have a link ready yet to an external supplier of chemicals as you asked in your request. In case of a special request of a chemical compound we could suggest www.chemie.de as a source to search for different suppliers who offers the compound. To learn more about SPRESIweb we offer you a free test account for four weeks to SPRESIweb. Just let us know whenever you like to test it. We are pleased to help you. Hope this information is helpful for you Best Regards Claudia Pick and the SPRESIweb Team maybridge http://www.maybridge.com/ provides online search of its compound database regards Fabien Hi Donald, I recall receiving a free CD from MDD with a database of virtually available compounds collected from hundreds of companies and universities around the world - maybe it could be of use? Their website is www.worldmolecules.com /Mads Hi Donald, here is a list of some companies selling chemical compounds. I think all of them provide their libraries in SD/MDL format for download or on CD. Of course you still need a program to do the search. We use commercial software, but I'm sure there are cheap or even free alternatives, at least to do some of the simpler things. I hope this helps, Uwe InterBioScreen ChemicalDiversity IFLAB ComGenex Nanosyn TimTec Aldrich TimTech SIGMA FLUKA BioNet Pharmeks OrionResearch TosLab Asinex Maybridge Specs Tripos Chembridge Hi Don, Try ChemNavigator at www.chemnavigator.com (you have to register). You'll get access to more than 12 million chemical samples, a search interface, and all info to order compounds. Cheers, Sorel.