---
Osman F. G=FCner, Ph.D.
Sr. Director, Lead Identification & Optimization
Accelrys Inc. (858) 799-5341
osman@accelrys.com http://www.accelrys.= com --=====================_14952901==_.ALT-- From chemistry-request@server.ccl.net Thu Mar 7 16:30:50 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g27LUo514332 for ; Thu, 7 Mar 2002 16:30:50 -0500 Received: from cer.yubc.net (cer.yubc.net [212.124.160.3]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id QAA26261 for ; Thu, 7 Mar 2002 16:30:47 -0500 (EST) From: ssgrr2002s@rti7020.etf.bg.ac.yu Received: from avala.yubc.net (avala.yubc.net [212.124.160.1]) by cer.yubc.net (8.9.3/8.9.3) with ESMTP id WAA21830 for ; Thu, 7 Mar 2002 22:29:45 +0100 Received: (from root@localhost) by avala.yubc.net (8.9.3/8.9.3) id WAA24442 for chemistry@ccl.net; Thu, 7 Mar 2002 22:29:45 +0100 Date: Thu, 7 Mar 2002 22:29:45 +0100 Message-Id: <200203072129.WAA24442@avala.yubc.net> To: chemistry@ccl.net Subject: Invitation to be a speaker at the SSGRR 2002s Conference in L`Aquila near Rome, Italy (Jul 29 - Aug 4 2002.) Honorable Professor, I have been appointed to serve as the General Chair of the Summer 2002 edition of the SSGRR series of international conferences, and I would like to extend a special invitation to you. The SSGRR-2002S (Summer) conference on "Infrastructure for e-Business, e-Education, e-Science, and e-Medicine" takes place in SSGRR (Scuola Superiore G. Reiss Romoli), the delux congress and educational center of the Telecom Italia Group of companies. This is in L'Aquila near Rome, Italy, from July 29 (Monday) at 5pm (start of the Grand Opening) till August 4 (Sunday) at 10am (departure of busses to the Rome airport Fiumicino and the railway station Tiburtina). Most of the past participants beleive that this was one of the most interesting, most useful, and definitely THE most hospitable conference they ever attended. The SSGRR-2002S will be open by Jerome Friedman from MIT (laureate of the NOBEL PRIZE) and Travor Gruen-Kennedy of Citrix (listed by some sources, together with Bill Gates, as one of the world's TOP-25 contributors to the development of the Internet). For details, see the WWW site of the conference (www.ssgrr.it/en/ssgrr2002s/index.htm). Among other things, this WWW site also includes the full-blown version of the invitation letter-contract, with all relevant details (www.ssgrr.it/en/ssgrr2002s/invitation.htm). The soft deadline for you to decide if you are coming is March 25, 2002 (in the worst case you should respond before March 31st). By that date the place for you is unconditionally reserved. After that date, you will be accepted to the conference only if the existing 240 places are not filled. Before March 25, 2002, please send only the following: (a) TITLE, (b) AUTHORS, (c) AFFILIATION, (d) ABSTRACT, and (e) STATEMENT THAT YOU WILL COME 100% (answers like "maybe" will be treated as NO answer from you). The full paper is due on May 31, 2002. The early registration price for the 6-day stay at SSGRR is EURO1200 (if you represent an institution) or EURO1440 (if you come as an individual). Coming without a paper costs you extra EURO600 or EURO720, respectively. Deadline for the early registration is June 30, 2002. If you come with an accompanying person, the early registration extra cost is EURO300, for 6 days of bed and breakfast, in an external hotel (please note that the best external hotels are 4-star, and not nearly as comfortable as the accomodation in the SSGRR complex). The SSGRR complex includes only single-bed rooms, and therefore available only to those who come without an accompanying person. If you have any questions, please check the WWW site of the conference and especially the part entitled FAQ(Frequently Asked Questions). If you still have questions or there is something that we can do for you, please write to Organizing Committee at ssgrr2002s@rti7020.etf.bg.ac.yu (preferred) or if absolutely neccessary, to myself directly (vm@etf.bg.ac.yu). Sincerely yours, Professor V. M. Milutinovic, General Chair of the SSGRR-2002S (galeb.etf.bg.ac.yu/~vm/) P.S. No matter if you will attend the SSGRR-2002S conference or not, please let us know if you like to be invited to the Winter edition of the year 2003 (SSGRR-2003W) to be held in the same place > from January 6, 2003 at 5pm till January 12, 2003 at 10am. Shall we reinvite you? Of course, if you wish not to receive again information about the SSGRR conferences, please let us know, and we will remove your name from our list. IMPORTANT DETAILS: 1. We invite participants from three groups: A: Researchers from the list of the most referenced scientists B: VIPs of succesfull high-tech companies C: Young talent (according to the criteria of the Organizing Committee) We try to maximaze the synergistic interraction among these 3 groups. 2. Your presentation is 25 minutes, plus 5 minutes for discussion and the change of speakers. 3. The author of the LAST paper in the session is the session chairman, so he/she is motivated to respect the timing. The slots of the non-show-up papers are to be used for extra discussions. Moving of presentation slots is NOT permitted. 4. Timing of the session is given on the WWW site of the conference. 5. More information on the SSGRR center is given on the WWW site of the conference. 6. Transportation related information, on July 29 from Tiburtina station in Rome to SSGRR in L'Aquila, and on August 4 from L'Aquila to Tiburtina station and Fiumicino airport is given in the conference WWW site (pay attention to FAQ). 7. Details of the food schedule, social program, and all other relevant details are also given on the WWW site of the conference. From chemistry-request@server.ccl.net Fri Mar 8 05:17:16 2002 Received: from fletxa.iqs.es (root@[193.145.86.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28AHF506155 for ; Fri, 8 Mar 2002 05:17:15 -0500 Received: from edurne.iqs.es (edurne.iqs.url.es [193.145.86.6]) by fletxa.iqs.es (8.9.3/8.9.3) with ESMTP id MAA29082 for ; Fri, 8 Mar 2002 12:20:54 +0100 Sender: rosalia@fletxa.iqs.es Message-ID: <3C4F39A9.594D9B6@edurne.iqs.es> Date: Wed, 23 Jan 2002 23:31:05 +0100 From: Rosalia Pascual X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: modeling loops of a GPCR Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit We are modeling the loops of a GPCR with the modeller program, however we are having problems with the N- anc C-terminal chains. We have also looked some other programs to model the loops with ab initio methodologies as Rosetta, however we are not quite satisfied with the results. We would be very thankful for some advice about alternative methodologies and programs. Thanks in advance. Rosalia *************************************************************************** Ramon Llull University (www.url.edu) Institut Quimic de Sarria -Organic Chemistry Department Via Augusta 390 08017- Barcelona, Spain Tel.: +34-93-267.20.00 *************************************************************************** From chemistry-request@server.ccl.net Fri Mar 8 12:22:05 2002 Received: from ccl.net ([192.148.249.4]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28HM5515507 for ; Fri, 8 Mar 2002 12:22:05 -0500 Received: from metalo2.iem.csic.es (metalo2.iem.csic.es [161.111.20.37]) by ccl.net (8.9.3/8.9.3/OSC 2.0) with ESMTP id MAA23898 for ; Fri, 8 Mar 2002 12:22:03 -0500 (EST) Received: from metalo2.iem.csic.es (metalo2.iem.csic.es [161.111.20.37]) by metalo2.iem.csic.es (SGI-8.9.3/8.9.3) with ESMTP id SAA98517 for ; Fri, 8 Mar 2002 18:21:55 +0100 (CET) Sender: jrd@metalo2.iem.csic.es Message-ID: <3C88F332.65FB0921@metalo2.iem.csic.es> Date: Fri, 08 Mar 2002 18:21:55 +0100 From: Javier Ramos Organization: CSIC X-Mailer: Mozilla 4.7C-SGI [en] (X11; I; IRIX64 6.5 IP30) X-Accept-Language: en MIME-Version: 1.0 To: chemistry@ccl.net Subject: problem with scan calculation Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Dear users, I would like to perform a scan calculation with gaussian 98. I have an ethylene molecule and I want to approach it to active site. I want to take the distance between the active site and the midpoint of the ethylene as reaction coordinate. How could I define this midpoint? Thanks Javier From chemistry-request@server.ccl.net Fri Mar 8 06:01:40 2002 Received: from mailrelay1.lrz-muenchen.de ([129.187.254.101]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28B1d507121 for ; Fri, 8 Mar 2002 06:01:39 -0500 Received: from sun4.lrz-muenchen.de by mailrelay1.lrz-muenchen.de with ESMTP for chemistry@ccl.net; Fri, 8 Mar 2002 12:00:47 +0100 Received: from localhost (ui22204@localhost) by sun4.lrz-muenchen.de (8.8.8+Sun/8.8.8) with ESMTP id MAA09684 for ; Fri, 8 Mar 2002 12:00:45 +0100 (MET) X-Authentication-Warning: sun4.lrz-muenchen.de: ui22204 owned process doing -bs Date: Fri, 8 Mar 2002 12:00:45 +0100 (MET) From: Eugene Leitl X-X-Sender: ui22204@sun4.lrz-muenchen.de To: chemistry@ccl.net Subject: FYI: superlinear speedups in GROMACS Message-Id: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII ---------- Forwarded message ---------- Date: Thu, 7 Mar 2002 23:24:49 -0500 From: 'Velocet' To: Jim Fraser Cc: beowulf@beowulf.org Subject: Re: DUAL CPU board vs 2 Single CPU boards: bang for buck? On Thu, Mar 07, 2002 at 12:45:26PM -0500, Jim Fraser's all... > Amazing. 1 cpu 63 ps/day, 2 cpu = 179 ps/day, sounds like a case of 1 + 1 = > 2.84 (ie. 63 + 63 = 179 (not 126)?) > Sounds fishy to me but I am unfamiliar with your application. Ask David VanDerSpoel, he'll tell you that they see superlinear speedups in Gromacs jobs quite often. Has to do with the cache, I'd guess something like with one CPU the job cant fit in L2 cache by itself, so lots of main memory accesses are required - when the job is split for 2 cpus, more of the job is in L2 caches, and despite the shared memory that LAM uses for communications for dual nodes, the overhead for that doesnt outweigh the advantage of having the job divided into more cache ram... works out well! :) It happens sometimes - they see 20-25% for Pentium (3? 4?) in speedups, but Athlons really kick ass for CERTAIN JOBS in gromacs (small jobs dont do this because one CPU is enough for the whole job, and MONSTER jobs may well be too big for the cache to give a big advantage - and once you go onto a network it may too slow to take advantage of directly (dotn know if people have scali numbers for gromacs 3.0 on Dual athlons >=1.2GHz) - I see >100% scaling per CPU with 4 nodes with GBE with that job (d.dppc) in gromacs 3.0 with 1.333 Ghz CPUs. [ im not sure this is all how it works, perhaps someone on the list can explain it. ] Go read the factoring hack by DJB I think it was that makes RSA style public key easier by a magnitude or so (couple weeks ago) - there are big speedups for that stuff due to multiple CPU cache usage... it seems somewhat related. /kc > Jim > > -----Original Message----- > From: beowulf-admin@beowulf.org [mailto:beowulf-admin@beowulf.org]On > Behalf Of Velocet > Sent: Thursday, March 07, 2002 11:00 AM > To: beowulf@beowulf.org > Subject: Re: DUAL CPU board vs 2 Single CPU boards: bang for buck? > > > On Thu, Mar 07, 2002 at 07:24:08AM -0500, Jim Fraser's all... > > I don't desire to start a flame but it seems to me that for computational > > intensive and memory intensive work that 2 singles are better and in most > > cases cheaper then a dual setup. The dual SMP systems out there now have > to > > fight for bandwidth along the same bus. The AMD chips while fast appear > to > > be starved for data when *big* memory jobs are running. Further I don't > see > > the cost benefits, if you actually dig into the "bang-for-buck" duals > never > > seem to win. > > Counter example: > > d.dppc on gromacs 3.0 calculation on a dual tyan 2460 board: > > 1 cpu 63 ps/day > dual cpu 179 ps/day > > cache, baby. > > now, if only we could get 8 way athlons! > > /kc > > > The only significant benefit I see from dual is less hardware and higher > > computing density, that may be reason enough to go with duals esp. if your > > application does not require a lot of memory fetches. > > > > > > Jim Fraser > > > > _______________________________________________ > > Beowulf mailing list, Beowulf@beowulf.org > > To change your subscription (digest mode or unsubscribe) visit > http://www.beowulf.org/mailman/listinfo/beowulf > > -- > Ken Chase, math@velocet.ca * Velocet Communications Inc. * Toronto, > CANADA > _______________________________________________ > Beowulf mailing list, Beowulf@beowulf.org > To change your subscription (digest mode or unsubscribe) visit > http://www.beowulf.org/mailman/listinfo/beowulf > -- Ken Chase, math@velocet.ca * Velocet Communications Inc. * Toronto, CANADA _______________________________________________ Beowulf mailing list, Beowulf@beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf From chemistry-request@server.ccl.net Fri Mar 8 12:41:00 2002 Received: from postoffice.mail.cornell.edu ([132.236.56.7]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28Hf0516030 for ; Fri, 8 Mar 2002 12:41:00 -0500 Received: from cornell.edu (sweet1.foodsci.cornell.edu [132.236.147.65]) by postoffice.mail.cornell.edu (8.9.3/8.9.3) with ESMTP id MAA13614; Fri, 8 Mar 2002 12:40:22 -0500 (EST) Sender: dwood@cornell.edu Message-ID: <3C88EDB4.1A31E1DA@cornell.edu> Date: Fri, 08 Mar 2002 11:58:28 -0500 From: "Dr. Richard L. Wood" X-Mailer: Mozilla 4.75C-SGI [en] (X11; I; IRIX 6.5 IP32) X-Accept-Language: en MIME-Version: 1.0 To: "chemistry@ccl.net" Subject: CHARMm pressure.doc Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hi all We are still having trouble determing pressures from CHARMm clacluations. So we've done a test on a 512 molecule box of water that has a density of about 1 g/cm^3. The volume of this box is 15366.93394 Angstroms^3. I've run a 20 ps Verlet dynamics simulation on thes waters using periodic boundary conditions. In the document pressure.doc, I came across a way to calculate the instantaneous pressures from my trajectory. Below is the code I used: ================================================= SET NTOT = 20 PRES INIT SET 1 1 LABEL LOOP TRAJ READ ENER PRES INST TEMP 300.0 NDEG 4608 VOLU 15366.9 INCREMENT 1 BY 1 IF 1 LE @NTOT GOTO LOOP PRES STAT ================================================= This outputs the instanteous pressure every ps. Here's typical output: ================================================== ENER ENR: Eval# ENERgy Delta-E GRMS ENER INTERN: BONDs ANGLes UREY-b DIHEdrals IMPRopers ENER EXTERN: VDWaals ELEC HBONds ASP USER ENER IMAGES: IMNBvdw IMELec IMHBnd RXNField EXTElec ---------- --------- --------- --------- --------- --------- ENER> 0 -5242.80489 -26.35422 12.83038 ENER INTERN> 3.61295 0.04294 0.00000 0.00000 0.00000 ENER EXTERN> 496.00280 -4612.07359 0.00000 0.00000 0.00000 ENER IMAGES> 63.63298 -1194.02297 0.00000 0.00000 0.00000 ---------- --------- --------- --------- --------- --------- CHARMM> PRES INST TEMP 300.0 NDEG 4608 VOLU 15366.9 ------------------------------------------------------------------------------- Virial KE = -5582.52498 Volume = 15366.90000 External Virial = 179.98097 Internal Virial = 3541.70235 External Virial Tensor : xx 195.59347 xy -1.87098 xz 63.70288 yx 431.95006 yy 440.08007 yz -44.40888 zx 119.04395 zy -779.44679 zz -95.73063 Internal Virial Tensor : xx 3422.93484 xy 121.34689 xz -99.13260 yx 121.34689 yy 3836.55309 yz 49.65984 zx -99.13260 zy 49.65984 zz 3365.61912 External Pressure = -803.08860 Internal Pressure = 19889.25317 External Pressure Tensor: xx -872.75275 xy 8.34845 xz -284.24702 yx -1927.39358 yy -1963.67029 yz 198.15574 zx -531.18305 zy 3477.95008 zz 427.15725 ------------------------------------------------------------------------------- ====================================================== As can be seen, the internal pressure is 19889.25317 atm, which seems rather large to me. The average for the entire 20 ps run is about 20000 atm. Now I know the CHARMm units of pressure are in atm, and the volume is in Angstroms^3. Is there some kind of conversion or something that I'm missing? I did a back of the envelope calculation and this many waters treated as an ideal gas at 300 K would only have a pressure of about 1366 atm, which is still large. Any help will be appreciated! Richard -- Richard L. Wood, Ph. D. Physical/Computational Chemist Post-doctoral Associate Department of Food Science 120 Stocking Hall Cornell University, Ithaca, NY 14853 From chemistry-request@server.ccl.net Fri Mar 8 12:58:17 2002 Received: from tigre ([158.109.14.43]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28HwF516464 for ; Fri, 8 Mar 2002 12:58:16 -0500 Received: from gali by tigre with local (Exim 3.12 #1 (Debian)) id 16jOc3-0003ah-00 for ; Fri, 08 Mar 2002 18:57:03 +0100 Date: Fri, 8 Mar 2002 18:57:03 +0100 From: Gali Drudis i Sole To: CCL Subject: ONIOM DFT/AM1 calculations with Osmium Message-ID: <20020308185703.A13746@tigre.qf.uab.es> Mail-Followup-To: CCL Mime-Version: 1.0 Content-Type: text/plain; charset=iso-8859-1 Content-Disposition: inline Content-Transfer-Encoding: 8bit User-Agent: Mutt/1.2.5i Sender: Debian User I am trying to calculate a large molecule using a hybrid method. The molecule contains an osmium tetroxide plus a large organic residue. The procedure will involve an ONIOM calculation using a small DFT region plus a large semiempiric region. However, the ONIOM method requires that the whole molecule be described by the low method, AM1 in this case. The problem arises when I try to calculate the whole molecule using AM1. To my unluck, not only is Osmium not parametrized in Gaussian98.A9, but the VSTO-3G basis does not suppor athoms greater than N=54 (osmium has an atomic number of 76). To make things worse, looking inside the code, every athom with N>54 is exchanged by Xe in link 301. But Xenon is described without d orbitals, and therefore I get the following error: ======================================================================== (Enter /QFsoft/g98/l301.exe) Standard basis: VSTO-3G (5D, 7F) Atomic number 76 exceeds maximum of 54 in STO -- maximum used. There are 5 symmetry adapted basis functions of A' symmetry. There are 1 symmetry adapted basis functions of A" symmetry. Crude estimate of integral set expansion from redundant integrals=1.000. Integral buffers will be 262144 words long. Raffenetti 1 integral format. Two-electron integral symmetry is turned on. 6 basis functions 18 primitive gaussians 5 alpha electrons 5 beta electrons nuclear repulsion energy 5.0493269225 Hartrees. Leave Link 301 at Fri Mar 8 18:49:55 2002, MaxMem= 6291456 cpu: 0.1 (Enter /QFsoft/g98/l401.exe) Simple Huckel Guess. NBasis= 6 NMin= 11 so simple Huckel guess is impossible. Error termination via Lnk1e in /QFsoft/g98/l401.exe. ======================================================================== Link 401 complains that not enough basis functions are available. Do you have any hint how I could solve this problem? Many thanks in advance, -- Gal� Drudis i Sol� gali@klingon.uab.es Universitat Aut�noma de Barcelona Unitat de Qu�mica Lab: C7/157 Tel: +34 93-581.28.14 Fax: +34 93-581.29.20 From chemistry-request@server.ccl.net Fri Mar 8 12:44:41 2002 Received: from prserv.net ([32.97.166.31]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28Hif516140 for ; Fri, 8 Mar 2002 12:44:41 -0500 Received: from attglobal.net (slip-32-100-104-167.ct.us.prserv.net[32.100.104.167]) by prserv.net (out1) with SMTP id <2002030817440420103e2cise>; Fri, 8 Mar 2002 17:44:04 +0000 Message-ID: <3C88F81A.4FA84518@attglobal.net> Date: Fri, 08 Mar 2002 12:42:50 -0500 From: reckon.dat@attglobal.net Reply-To: reckon.dat@attglobal.net X-Mailer: Mozilla 4.7 [en] (Win98; U) X-Accept-Language: en MIME-Version: 1.0 To: Computers in Chemistry Subject: 2002 Hansch Award Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit FIRST NOTICE Deadline for submitting candidates for the Hansch Award is 3 August 2002. Call for Nominees for the third Annual Hansch Award The award consists of $1000 (USD), and will be presented to the winner at the 14th European Symposium on QSAR in Bournemouth, UK, during the week of 8-13 September 2002. Last year�s winner was Gabriele Cruciani (University of Perugia). The winner in 2000 was Hua Gao (Pharmacia). Qualifications: � A person under the age of 40 years, � who is active in the field of Quantitative Structure-Activity Relationships, and � who has contributed significantly to the field. QSAR is defined broadly, in the same sense that we include papers and posters at the European Symposium on QSAR and the Gordon Research on QSAR. Hence, those who deal with drug design, physical properties, topological indices, molecular models, docking, protein folding, 3D-QSAR, combinatorial library design, similarity analyses, multivariate statistical analyses, and related topics are eligible. In short, any quantitative connection between biological or physical properties and chemical structure that requires computational techniques is appropriate. To nominate a candidate, please submit: � a resume of the nominee�s career, not more than two pages, � a bibliography of the nominee (as long as necessary), � no more than three reprints of the nominee�s key publications, i.e., those that form the basis of the nomination, and � a statement (not more than one page) from the nominator as to why his or her candidate deserves the award. Send these documents to: Dr. J. W. McFarland at one of the addresses given below. In submitting documents, the nominator should not assume that each of the committee members is aware of the nominee�s accomplishments. In cases where the nominee is or has been a member of a well-known and respected research group, there is a danger that the nominee�s contributions may not be easily distinguished from those of his or her mentor. Please, indicate how the nominee�s contributions are more than an obvious extension of his or her mentor�s. A statement from the mentor is acceptable as an additional document. The final decision will be made by a committee of five experienced workers in the field of QSAR. This announcement is being sent via different mailing lists. You may receive a duplicate. For the committee, J. W. McFarland, Chairman reckon.dat consulting 217 Blood Street Lyme, CT 06371-3509, U.S.A. fax to (860) 434-5125 e-mail: reckon.dat@attglobal.net. From chemistry-request@server.ccl.net Fri Mar 8 14:29:42 2002 Received: from mercury.chem.northwestern.edu (fparnold@[129.105.116.2]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28JTg519485 for ; Fri, 8 Mar 2002 14:29:42 -0500 Received: from localhost (fparnold@localhost) by mercury.chem.northwestern.edu (8.11.3/8.11.3) with ESMTP id g28JSbM23030; Fri, 8 Mar 2002 13:28:37 -0600 (CST) Date: Fri, 8 Mar 2002 13:28:37 -0600 (CST) From: "Fred P. Arnold" To: Eugene Leitl cc: Subject: Re: CCL:FYI: superlinear speedups in GROMACS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII We saw benchmarks of GAMESS-US on the IBM SP2 years ago that did this. Same issue; eventually the pieces are small enough to fit into cache, and it takes off like a shot, as long as communication overhead doesn't begin to dominate the calculation. -Fred Frederick P. Arnold, Jr. NUIT, Northwestern U. f-arnold@northwestern.edu From chemistry-request@server.ccl.net Fri Mar 8 14:34:55 2002 Received: from hermes.bmc.uu.se ([130.238.39.245]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28JYs519753 for ; Fri, 8 Mar 2002 14:34:54 -0500 Received: from XRAY.bmc.uu.se ([130.238.37.10]) by hermes.bmc.uu.se (Post.Office MTA v3.5.3 release 223 ID# 0-62649U1500L1000S0V35) with ESMTP id se for ; Fri, 8 Mar 2002 20:34:14 +0100 Received: from zorn.bmc.uu.se (IDENT:spoel@zorn.bmc.uu.se [130.238.37.95]) by XRAY.bmc.uu.se (8.11.6/8.8.7) with ESMTP id g28JYpb12891 for ; Fri, 8 Mar 2002 20:34:51 +0100 Date: Fri, 8 Mar 2002 20:34:03 +0100 (CET) From: David van der Spoel X-Sender: spoel@zorn.bmc.uu.se cc: chemistry@ccl.net Subject: Re: CCL:FYI: superlinear speedups in GROMACS In-Reply-To: Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII On Fri, 8 Mar 2002, Eugene Leitl wrote: >Ask David VanDerSpoel, he'll tell you that they see superlinear speedups >in Gromacs jobs quite often. Has to do with the cache, I'd guess something >like with one CPU the job cant fit in L2 cache by itself, so lots of >main memory accesses are required - when the job is split for 2 cpus, >more of the job is in L2 caches, and despite the shared memory that LAM >uses for communications for dual nodes, the overhead for that doesnt outweigh >the advantage of having the job divided into more cache ram... works >out well! :) It works on IBM Sp2 as well, and is very nice indeed on Scali networks: http://www.gromacs.org/benchmarks/scaling.php Our memory access pattern is "quite serial", but not entirely, that's why the cache improves performance so much. Groeten, David. ________________________________________________________________________ Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry Husargatan 3, Box 576, 75123 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 spoel@xray.bmc.uu.se spoel@gromacs.org http://zorn.bmc.uu.se/~spoel ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From chemistry-request@server.ccl.net Fri Mar 8 14:37:43 2002 Received: from lauca.usach.cl ([158.170.64.28]) by server.ccl.net (8.11.6/8.11.0) with ESMTP id g28Jbg519911 for ; Fri, 8 Mar 2002 14:37:42 -0500 Received: from danilo ([158.170.51.186]) by lauca.usach.cl (8.10.2+Sun/8.10.2) with ESMTP id g28JYce01933 for ; Fri, 8 Mar 2002 16:34:39 -0300 (CLST) From: "Danilo Gonzalez" To: Subject: CHARMM FEP example Date: Fri, 8 Mar 2002 16:34:12 -0300 Message-ID: <004e01c1c6d8$3b607fa0$ba33aa9e@usach.cl> MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="----=_NextPart_000_004F_01C1C6BF.161347A0" X-Priority: 3 (Normal) X-MSMail-Priority: Normal X-Mailer: Microsoft Outlook, Build 10.0.2627 X-MimeOLE: Produced By Microsoft MimeOLE V5.50.4807.1700 Importance: Normal This is a multi-part message in MIME format. ------=_NextPart_000_004F_01C1C6BF.161347A0 Content-Type: text/plain; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable Hi all! =20 I=92m looking for some examples of FEP calculation using CHARMm. I will appreciate any information about FEP calculation, or any other examples, using CHARMm. =20 Thanks a lot again! =20 Danilo Gonzalez-Nilo =20 University of Santiago of Chile Faculty of Chemistry and Biology Casilla 40, Correo 33, Santiago - Chile. =20 ------=_NextPart_000_004F_01C1C6BF.161347A0 Content-Type: text/html; charset="Windows-1252" Content-Transfer-Encoding: quoted-printable

Hi all!

I=92m looking for some examples of FEP calculation = using CHARMm. I will appreciate any information = about FEP calculation, or any other examples, using CHARMm.

Thanks a lot again!

Danilo = Gonzalez-Nilo

University of Santiago of Chile<= span style=3D'mso-no-proof:yes'>

Faculty of Chemistry and = Biology

Casilla 40, Correo = 33,

Santiago - = Chile<= span style=3D'mso-no-proof:yes'>.