From owner-chemistry@ccl.net Sat Mar 18 07:17:00 2006 From: "Jeff Nauss jnauss..accelrys.com" To: CCL Subject: CCL: A review of force fields Message-Id: <-31235-060318070514-8659-MPAhSLEouPjNNFECenVanA__server.ccl.net> X-Original-From: Jeff Nauss Content-Type: text/plain; charset="US-ASCII" Date: Sat, 18 Mar 2006 04:04:56 -0800 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss[-]accelrys.com] Loan Huynh [huynhkl2000{:}yahoo.ca] wrote on 03/16/2006 09:27:16 AM: > I would like to gain knowlegde on force fields that are recently > used for the molecular dynamics. Does anyone know if there is a > review on the force field that are populated recently? From my > understanding, there is force field that is appropriate for > macromolecular (i.e polymer), or force filed for protien, or small > molecules ... I find these references useful for small molecule comparisons. Gundertofte et al. J. Comp. Chem. 1996, 17:429-49 Pettersson & Liljefors Rev. Comp. Chem. 1996, 9:167-90 Nicklaus, J. Comp. Chem. 1997, 18:1056-60 Halgren, J. Comp. Chem. 1999, 20:730-748 For proteins there is also this reference: Price DJ, Brooks CL, III. 2002. Modern protein force fields behave comparably in molecular dynamics simulations. J Comp Chem 23: 1045 Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training From owner-chemistry@ccl.net Sat Mar 18 11:54:00 2006 From: "Eugen Leitl eugen|-|leitl.org" To: CCL Subject: CCL:G: [Beowulf] G03 in Linux cluster Message-Id: <-31236-060318070514-2-wi47wHlGVshWe6S2xH7wtg[]server.ccl.net> X-Original-From: Eugen Leitl Date: Sat, 18 Mar 2006 09:33:34 +0100 Sent to CCL by: Eugen Leitl [eugen * leitl.org] ----- Forwarded message from Jess Cannata ----- >From: Jess Cannata Date: Fri, 17 Mar 2006 14:08:32 -0500 Cc: Beowulf||beowulf.org Subject: Re: [Beowulf] [owner-chemistry||ccl.net: CCL:G: parallel G03 in Linux cluster] User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.12) Gecko/20050915 Eugen Leitl wrote: >Hello Everybody, > >I am planning to buy sixteen AMD64 Athlon dual core machines (with >Linux) for running G03 in parallel. They will be connected by ethernet. >I never have any experience in running gaussian with Linux cluster. So >my questions are the following: > >1. Can G03 be run parallel in the above configuration? >2. Do you need to have Linda for running parallel in the above >configuration? > > You need Linda to run G03 in parallel. >3. Do you recommend any other processor? > > We run G03 on both Xeon and Opteron Beowulf Clusters and are very pleased with the Opterons. >4. Which brand of Linux is good for running G03 parallel? > > This depends on whether you have the binary or source code version. If you use the binaries, you should follow Gaussian's recommendations. We run G03 (64-bit) on SuSE 9.0 and RedHat AS 4 without any problems. >5. Pals sharer your experience with running G03 parallel in Linux >cluster (like tricks, problems, failure etc). > > Good luck! G03 can be finicky. Jess >Thanks in advance >Debasis > > > _______________________________________________ Beowulf mailing list, Beowulf||beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf ----- End forwarded message ----- -- Eugen* Leitl leitl http://leitl.org ______________________________________________________________ ICBM: 48.07100, 11.36820 http://www.ativel.com 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE [CCL Admin removed application/* MIME attachment] From owner-chemistry@ccl.net Sat Mar 18 12:29:00 2006 From: "Eugen Leitl eugen-#-leitl.org" To: CCL Subject: CCL:G: [Beowulf] CCL:G: parallel G03 in Linux cluster Message-Id: <-31237-060318070514-1-/ZxpWnhJm1+i0bjWcj837w ~~ server.ccl.net> X-Original-From: Eugen Leitl Date: Sat, 18 Mar 2006 09:33:46 +0100 MIME-Version: 1.0 Sent to CCL by: Eugen Leitl [eugen**leitl.org] >From: Reuti Date: Fri, 17 Mar 2006 23:29:31 +0100 To: Jess Cannata Cc: Beowulf!A!beowulf.org Subject: Re: [Beowulf] [owner-chemistry!A!ccl.net: CCL:G: parallel G03 in Linux cluster] User-Agent: Internet Messaging Program (IMP) H3 (4.0.3) Quoting Jess Cannata : >Eugen Leitl wrote: > >>Hello Everybody, >> >>I am planning to buy sixteen AMD64 Athlon dual core machines (with >>Linux) for running G03 in parallel. They will be connected by >>ethernet. I never have any experience in running gaussian with Linux >>cluster. So my questions are the following: >> >>1. Can G03 be run parallel in the above configuration? >>2. Do you need to have Linda for running parallel in the above >>configuration? >> >You need Linda to run G03 in parallel. The OpenMP parallelization should also work without Linda - but of course limited to some routines and 2 cores. > >>3. Do you recommend any other processor? >> >We run G03 on both Xeon and Opteron Beowulf Clusters and are very >pleased with the Opterons. > >>4. Which brand of Linux is good for running G03 parallel? >> >This depends on whether you have the binary or source code version. >If you use the binaries, you should follow Gaussian's >recommendations. We run G03 (64-bit) on SuSE 9.0 and RedHat AS 4 >without any problems. > >>5. Pals sharer your experience with running G03 parallel in Linux >>cluster (like tricks, problems, failure etc). >> >Good luck! G03 can be finicky. For a Tight Integration into SGE I put some hints on their list (if you intend to use a queuing system): http://gridengine.sunsource.net/servlets/ReadMsg?listName=users&msgNo=7317 http://gridengine.sunsource.net/servlets/ReadMsg?listName=users&msgNo=14600 and worth to note a 3rd party hint: http://gridengine.sunsource.net/servlets/ReadMsg?listName=users&msgNo=14603 HTH - Reuti > >Jess > >>Thanks in advance >>Debasis >> >> >_______________________________________________ >Beowulf mailing list, Beowulf!A!beowulf.org >To change your subscription (digest mode or unsubscribe) visit >http://www.beowulf.org/mailman/listinfo/beowulf > _______________________________________________ Beowulf mailing list, Beowulf!A!beowulf.org To change your subscription (digest mode or unsubscribe) visit http://www.beowulf.org/mailman/listinfo/beowulf ----- End forwarded message ----- Eugen* Leitl http://leitl.org _____________________________________________________________ ICBM: 48.07100, 11.36820 http://www.ativel.com 8B29F6BE: 099D 78BA 2FD3 B014 B08A 7779 75B0 2443 8B29 F6BE [CCL Admin removed application/* MIME attachment] From owner-chemistry@ccl.net Sat Mar 18 13:04:00 2006 From: "Abhishek Jha ajha-.-midway.uchicago.edu" To: CCL Subject: CCL: A review of force fields Message-Id: <-31238-060316205408-30259-JNfsBtS0GKXNRP8Fscb4Qg .. server.ccl.net> X-Original-From: Abhishek Jha Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Thu, 16 Mar 2006 14:13:06 -1100 MIME-Version: 1.0 Sent to CCL by: Abhishek Jha [ajha^_^midway.uchicago.edu] Hello LH: You might find this paper useful. Zaman 2003 JMB 331 693-711. Thanks, AJ From owner-chemistry@ccl.net Sat Mar 18 13:38:01 2006 From: "Sengen Sun sengensun%%yahoo.com" To: CCL Subject: CCL: Very important questions Message-Id: <-31239-060318130952-18035-LtriY4+D5vnyEXHa/FnwCg{}server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sat, 18 Mar 2006 10:09:48 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun+*+yahoo.com] Thanks to every one for patience. I have received quite a number of e-mails of tremendous interests. Several people have to wait for a few days for me to get back to them. I have to continue the public discussion as soon as there are outstanding issues to be addressed. But I will try my best to limit my posts. This post is a very important one. Here are extremely important questions by Mateo: --- Mateo Alajarin wrote: > Dear Dr Sun > > You recently wrote (in a message to orglist): > > >I do not have a beter way to explain, but let me > give > >you recent one of particular examples of conceptual > >confusion made by Hoffmann (See JACS, 2002, 124, > 6836, > >Scheme 1, I will forward this article to any one if > >requested by e-mail). There, the intramolecular > proton > >transfer was mistakenly treated as hydride > transfer. > >That is, the arrows should be drawn in the exactly > >opposite direction. > > This paragraph caught specially my attention. May I > ask you why you believe > that the arrows in that Scheme should be drawn in > the opposite direction? > As far as you know, is there a rule (or a way, or a > parameter) for > identifying if, in a sigmatropic H shift between two > carbon atoms, the > migrating atom is more or less proton-like or > hydride-like? > > Thanks in advance for your answer, > > Mateo.- > > XXXXXXXXXXXXXXXXXXXX > Mateo Alajarin > Dep. Quimica Organica > Fac. Quimica > Universidad de Murcia > Campus de Espinardo > 30100 Murcia > Spain > Phone +34.968.367497 > Fax +34.968.364149 > email: alajarin^^um.es > XXXXXXXXXXXXXXXXXXXX > Mateo's questions are quite common in the community. But these questions are both very important and very weird! My question is why these questions should be questions? If you have good knowledge of general acid and general base in organic chemistry, you shouldn't ask these questions. Alkane C-H is a very weak hydrocarbonic acid, while CC pi electrons are a base. When they react, what definitely CANNOT happen is the hydride transfer from C-H to a CC pi bond no matter intermolecular or intramolecular with or without aromatic transition state. Are there cases that C-H bond reacts as a hydride donor? Yes. But it requires that the other reacting partner be much stronger general acid (or very electron-deficient). In general, proton transfer or hydride transfer really depends on a particular dynamic environment between two reactants. Why such basic knowledge has been made so messy? We have been driven insane by orbitals for decades! Another person asked a much harder question for the parent Diels-Alder reaction in my ppt presentation. In Organic Chemistry by Fox & Whitesell, it says that "the progression of this reaction is indicated by the full-headed curved arrows showing the motion of each electron pair as the p electrons of each reactant are delocalized in the cyclic, conjugated transition state". When I saw such a statement at the University of Chicago Bookstore in 1997, I bought the book immediately. I had never owned an organic chemistry textbook in English as I had not seen a good one. How did I know that Fox & Whitesell are surely right? Karadakov et al proposed a concerted spin-recoupling (JACS 1998, 120, 3975), but as a consequence of artificial effects of their computational approach! The problem is that we have denied the underlying physics of chemical reactions. As in my ppt presentation (if you have not seen it yet, http://www.ccl.net/cca/documents/ConcertedCycloadditons_2/), when two neutral molecules collide, the first physical event is electron-electron repulsion. When the e-e repulsion develops, the electrons will seek a more comfortable place to stay in order to avoid the repulsion. That is why the electron-pushing mechanism is justified. It is such a simple thing. We cheat ourselves by looking at the HOMO-LUMO interaction picture that does not mean anything. But the electron-pushing mechanism for the parent D-A reaction was NOT significantly recognised, because we could not understand any fundamental reasons of the regioselectivity in cycloadditions. That is why I have made a breakthrough here. For the parent D-A reaction, it is not possible to get some data to prove the electron-pushing mechanism based on our current computational and experimental techniques. But my computational data on other cycloadditions validate the e-e pushing mechanism indirectly. The intra- or inter-molecular proton transfer can be easily proved computationally. In the last century, I studied Alder-ene reactions such as that between ethene and propene that involves a proton transfer via an aromatic transition state. The data are still stored in one of my antique computers. I could not get anything published. The faults don't lie with any referees or editors but with our fundamentally wrong chemical reaction theories based on MOs. One referee asked, how do you know the electron flow is caused by electrostatic forces? I gave up with laughing -:) That is long enough. Thanks. Regards to all. Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com