From owner-chemistry@ccl.net Fri Dec 9 04:09:00 2005 From: "Ben Sattelle ben.sattelle[*]postgrad.manchester.ac.uk" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30247-051209040651-31672-xjzmDL7/S1jO0TH0++ZsCA##server.ccl.net> X-Original-From: Ben Sattelle Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-15; format="flowed" Date: Fri, 9 Dec 2005 09:06:12 +0000 MIME-Version: 1.0 Sent to CCL by: Ben Sattelle [ben.sattelle|*|postgrad.manchester.ac.uk] > 2. I have a docked complexes contains ligands and proteins. With > this, I may want to create a movie showing docking of a ligand into > the active site and save it in file. hi, this may or may not be useful. below is a howto for converting a CHARMM trajectory into an animated *.gif file. requires, VMD, PyMol & convert (imagemagik tool, comes with cygwin). ben. 1) load *.pdb file into VMD load *.dcd trajectory into VMD goto File->Save Coordinates select molecule choose 'Frames' for animation (say 10-50 in total for testing, see later) leaving 'stride' set to 1 worked for me under 'File type' select 'pdb' and then 'Save' you should now have a stack of structures in one (pdb) file 2) use this sed oneliner on the file to substitute END for ENDMDL globally, $ sed -e 's/END/ENDMDL/' infile.pdb > outfile.pdb outfile.pdb can now be read by PyMol 3) read outfile.pdb into PyMol and setup as you wish e.g. select fmn, resn fmn set stick_radius=0.15 select T57, resid 57 select A58, resid 58 select water, resn TIP3 4) issue the following at the PyMol command line mset 1 -50 /* ... if you have 50 frames, see mset in PyMol manual */ set ray_trace_frames=1 /* ... looks pretty! */ set cache_frames=0 /* ... save memory */ mclear /* ... clear memory */ mpng animationame /* ... go! */ this may take some time, go for a cup of coffee! processing 50 frames requires a few minutes on my pc, setting ray_trace_frames=0 should save time if you can't find the output (*.png files) in the cwd have a look in C:\Program Files\DeLano Scientific\PyMOL 5) cd to directory containing *.png files, use convert $ convert -delay 20 *.png animation.gif the -delay flag sets the time between frames (ms), other outfile formats are supported also, man convert the *.gif animations function within powerpoint (in presentation mode) and web browsers! From owner-chemistry@ccl.net Fri Dec 9 08:13:00 2005 From: "Kenneth Geisshirt kenneth],[geisshirt.dk" To: CCL Subject: CCL: Linux Cluster Building Workshops Message-Id: <-30248-051209080524-24165-gL5WTRaChA5SDV9U/Vcsuw##server.ccl.net> X-Original-From: Kenneth Geisshirt Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 09 Dec 2005 13:24:41 +0100 MIME-Version: 1.0 Sent to CCL by: Kenneth Geisshirt [kenneth=geisshirt.dk] Andrew D. Fant fant(~)pobox.com wrote: > O'Reilly, whose titles are > usually the last work for IT topics like this, has published 2 disappointing > volumes for this as well. The first was simply Building Linux Clusters and has > been withdrawn from the market. The follow-on "Building High-Performance Linux > Clusters" is better, but still is less that one might help. I will recommend "Building Clustered Linux Systems" by Robert W. Lucke. > If you simply want to put together 4-8 PCs to run a single application for you > or a single research group, I would suggest looking at Rocks ( > http://www.rocksclusters.org) as a simple way to get something up and running. The Rocks distribution is easy to get going. And it's a Red Hat based distro, many commercial software packages will be easy to install. Moreover, the many 3rd party package repositories (atrpms.net etc.) can be integrated and you will have access to a large code base. > My biggest bit of advice, however, comes from a bumper sticker that the > electrician's union hands out around here. "Wiring Is Not A Hobby". If you are > going to be running multiple applications from multiple sources/vendors, going > above about 10 systems, having users from more than one fairly tight-knit and > cooperative research group, or making the results from this cluster the basis > of your research plans, you probably want to get an IT professional involved. I can second that (I'm one of those IT professionals). Linux clusters ain't rocket science but the complexity can be huge. If you start from scratch you have to decide which Ethernet switch is best, how to wire the stuff (low level) and which policy to implement in your batch system (high level). If you build a cluster every second year it's almost impossible to keep up with the development in this area. An IT professional might build 5-6 clusters every year so pick his brain! /kneth From owner-chemistry@ccl.net Fri Dec 9 09:30:00 2005 From: "Jerome PANSANEL j.pansanel{}pansanel.net" To: CCL Subject: CCL: Linux Cluster Building Workshops Message-Id: <-30249-051209042211-10773-AWtiKxgMYgq4JhK82gvCDg]_[server.ccl.net> X-Original-From: Jerome PANSANEL Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-15" Date: Fri, 9 Dec 2005 09:36:39 +0100 MIME-Version: 1.0 Sent to CCL by: Jerome PANSANEL [j.pansanel[-]pansanel.net] I recommend this book for such workshop or anyone looking for more informations about HPC linux clusters: "High Performance Linux Clusters" edited by O'Reilly Jerome Pansanel Le Jeudi 08 Décembre 2005 22:37, himanshu khandelia hkhandel%%cems.umn.edu a écrit : > Sent to CCL by: "himanshu khandelia" [hkhandel- -cems.umn.edu] > Is anyone aware of any cluster building workshops that might be useful for > engineers and scientists who are not system administrators, but are trying > to build their own machines ? From owner-chemistry@ccl.net Fri Dec 9 10:05:00 2005 From: "Roy Jensen rjensen**consol.ca" To: CCL Subject: CCL:G: A question to educational workers Message-Id: <-30250-051209040911-32188-ZdXMSSfp7aPmcudTjUCBFg[*]server.ccl.net> X-Original-From: Roy Jensen Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Fri, 09 Dec 2005 02:09:03 -0700 MIME-Version: 1.0 Sent to CCL by: Roy Jensen [rjensen * consol.ca] All >My current questions are directed to those who teach >something like ["orbitals not physically real; >orbitals not observable; objections to that orbitals >observable"....] > >How do you folks explain to an average student when he >argues with you with copies of the Nature papers, >Science papers, C&EN news reports... that all have >positively confirmed orbital orbservations? My quandary stems from the multiple definitions of 'orbital'. IUPAC defines an orbital as the "one-electron wavefunction obtained as a solution of the Schrödinger equation for an atom." Other definitions include 1. "the space in an atom occupied by an electron, a subdivision of the available space within an atom for an electron to orbit the nucleus" 2. "a mathematical function used to describe the behavior of an electron in an atom" Definitions that focus on the mathematical function definition separate the orbital and the electron. Thus, THEY DO NOT CARE WHETHER THE ORBITAL IS OCCUPIED OR NOT. The alternate definition asserts that THE ELECTRON IS THE ORBITAL. Without an electron, there is no orbital. I am left with the following: a) Can you observe a mathematical function? Yes. b) Are multi-gaussian functions a reasonable MODEL for the probability density distribution of a single electron? No. c) Is a model real? No. d) Is the summation of one-electron functions the same as a multi-electron function? Only with full CI. e) Can you observe a single electron? Not in a multi-electron system. f) Can you observe the sum of all the electrons in a multi-electron system? Yes. I am interested in how others perceive this issue. Dr. Roy Jensen (==========)-----------------------------------------¤ Chemistry, Grant MacEwan College Edmonton, AB T5J 4S2 780.633.3915 On Thu, 8 Dec 2005 17:00:23 -0500, you wrote: >Sent to CCL by: Sengen Sun [sengensun|yahoo.com] >Dear college and graduate school educational workers: > >In the last January when we were in the hot debate, >one of you wrote me saying something like this: > >["My friend, orbitals will be observed again and again >and again..., first in Nature, then in Science, then >in JACS, then in JPC, JOC, JIC...... The images will >be very very pretty. I want to see by then how well >you like those images....."] > >My current questions are directed to those who teach >something like ["orbitals not physically real; >orbitals not observable; objections to that orbitals >observable"....] > >How do you folks explain to an average student when he >argues with you with copies of the Nature papers, >Science papers, C&EN news reports... that all have >positively confirmed orbital orbservations? > >Do you have to say ["Nature papers are wrong, Science >papers are wrong, C&EN news reports are wrong, Angew >Chem is wrong..... Please trust me, my rationale is >right because Hoffmann said something like orbitals >are both real and unreal. And Hoffmann also said that >PES tells us the ways orbitals interact..."]? > >Do you also have to tell the student finally that you >cannot understand this until you drink and digest all >deeplyu of the Pyrean (sic) spring? > >What else could you say? I am really curious. > > >We are facing an unbearable disaster and dilemma in >scientific education and research on this issue. This >why I have stood up to support Dr. Eric Scerri who >raised such an very important issue initially at CCL >years ago. > > > >I have received a private e-mail I like the most so >far, which says: ["You attacker are too naive if you >think all drivers are free of alcohol"]. How wanderful >such a metaphor! >The quote by Hoffmann has a clear language >word-by-word no matter how you read it. There has not >been so far a second person who dare to say explicitly >TRUE or FALSE to it in the public. How interesting it >is in the modern age of human civilization in science >and philosophy! > > >Sengen > > > > > >__________________________________________________ >Do You Yahoo!? >Tired of spam? Yahoo! Mail has the best spam protection around >http://mail.yahoo.com> > From owner-chemistry@ccl.net Fri Dec 9 10:40:01 2005 From: "Caio Lima Firme cfirme(a)iq.ufrj.br" To: CCL Subject: CCL: A question to educational workers Message-Id: <-30251-051209061136-7276-Js2CEeOoVpCBNynT8Z7pbw##server.ccl.net> X-Original-From: "Caio Lima Firme" Sent to CCL by: "Caio Lima Firme" [cfirme|*|iq.ufrj.br] Hi CCLers Special attention is paid to me on this molecular orbital debate. Despite the widespread success of molecular orbital theory, one thing should be remembered: Slater determinants do not take into account the correct permutation symmetry. Then, the orbitals generated by HF theory are unreliable in any sense you may want to direct your reasoning. Morever, bonding molecular orbitals have a frail connection to chemical sense of electron distribution in a many-particle molecule. A more reasonable rationale on orbitals is given by GVB and SCVB theories. They have a correct permutation symmetry calculated by Youngs tableaux and produce more chemically reliable orbitals. Before clarifying students about reality or not of orbitals, shouldnt we be teaching them all different theories related to orbitals? In one point we should be aware, most undergraduate text books (if not all) give MO all the credits to explain experimental results and the chemistry rationale. As cited above, MO has considerable limitations and chemistry teaching should pay more attention to VB theory, mainly GVB and SCVB. Best regards Caio Lima Firme PhD student Universidade Federal do Rio de Janeiro Instituto de Qumica e-mail: firme.caio() gmail.com From owner-chemistry@ccl.net Fri Dec 9 11:28:00 2005 From: "Jason Gans jgans*lanl.gov" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30252-051209112408-10428-rH58G18zdzVO3h5Jyc7j/w-*-server.ccl.net> X-Original-From: Jason Gans Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; format=flowed Date: Fri, 9 Dec 2005 08:39:01 -0700 Mime-Version: 1.0 (Apple Message framework v623) Sent to CCL by: Jason Gans [jgans{:}lanl.gov] Qmol (windows only, http://www.mbg.cornell.edu/Shalloway_Lab_QMOL.cfm) will make movies using a PDB and a DCD file or a PDB file will multiple structures. Regards, Jason On Dec 8, 2005, at 1:50 PM, ramesh r ramesh_ass]_[yahoo.co.in wrote: > Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in] > --0-41187699-1134060055=:97686 > Content-Type: text/plain; charset=iso-8859-1 > Content-Transfer-Encoding: 8bit > > Hi CCLers, > I have two questions to ask related to how to create a animation and > movie: > 1. I may want to create a animation of a molecular model protein > like rotation, translation and save it as file. > 2. I have a docked complexes contains ligands and proteins. With > this, I may want to create a movie showing docking of a ligand into > the active site and save it in file. > > At this point, Could you please suggest any program do that task. > > Thanks in advance > sincerely, > ramesh > > > > From owner-chemistry@ccl.net Fri Dec 9 13:29:00 2005 From: "Christopher Smith csmith~~ctbp.ucsd.edu" To: CCL Subject: CCL: CTBP 2006 Comp Chem/Bio Workshops Message-Id: <-30253-051209115346-31864-jJCu1/Z9yuXjR/b1m2LMug,server.ccl.net> X-Original-From: Christopher Smith Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 9 Dec 2005 07:50:00 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Christopher Smith [csmith]^[ctbp.ucsd.edu] The Center for Theoretical Biological Physics at the University of California, San Diego will be hosting two workshops next Summer - 2006. Quantitative Approaches to Gene Regulatory Systems July 9 - 21, 2006 Molecular Simulation and Structure Prediction using CHARMM and the MMTSB Tool Set July 31 - August 4, 2006 Although prospective participants need to apply for these workshops, there is no registration fee, and housing, meals and all or a portion of participants travel costs will be provided by CTBP. These workshops are designed for graduate students, post-docs, and junior faculty who are looking for an overview and practical, hands-on training in a variety of computational methods. For detailed information or to apply (online) to either of these workshops, point your web browser to http://ctbp.ucsd.edu, or contact: Christopher M. Smith, PhD., csmith,ctbp.ucsd.edu, 858-534-8370. -- Christopher M. Smith, PhD. Assoc Director for Education, Outreach & Training Center for Theoretical Biological Physics Department of Physics, University of California 9500 Gilman Drive, San Diego, CA 92093-0374 csmith,ctbp.ucsd.edu ctbp.ucsd.edu (858) 534-8370 (office) 858-245-4794 (cell) From owner-chemistry@ccl.net Fri Dec 9 14:04:00 2005 From: "Jozsef Csontos jozsefcsontos!^!creighton.edu" To: CCL Subject: CCL:G: Gaussian Compilation Message-Id: <-30254-051209125550-22395-6+E8RpCG4r9qfMCmEHcfpA..server.ccl.net> X-Original-From: Jozsef Csontos Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 09 Dec 2005 10:59:21 -0600 Mime-Version: 1.0 Sent to CCL by: Jozsef Csontos [jozsefcsontos-.-creighton.edu] Just, think about it :) "I prefer a capitalist approach (like peer reviewed journals and associated databases) where people know who's responsible and can take the action necessary to ensure accountability and success." (11/22/5) On Fri, 2005-12-02 at 09:26 -0500, Jim Kress ccl_nospam[A]kressworks.com wrote: > Sent to CCL by: "Jim Kress" [ccl_nospam- -kressworks.com] > No. Gaussian refuses to provide a significant level of support and > parasitically depends upon CCL to provide user to user problem resolution. > > Rather disgusting behavior for a company that charges thousands of dollars > for taxpayer funded work and then refuses to provide comprehensive support > for those products it has developed with money forcibly removed from other > people. > > Jim > > > -----Original Message----- > > From: Roger Kevin Robinson r.robinson~!~imperial.ac.uk > > [mailto:owner-chemistry(0)ccl.net] > > Sent: Friday, December 02, 2005 7:48 AM > > To: Kress, Jim > > Subject: CCL:G: Gaussian Compilation > > > > Sent to CCL by: "Roger Kevin Robinson" > > [r.robinson**imperial.ac.uk] Hi, > > > > Does any one know if there is a mailing list particualarly > > for Gaussian ? > > > > Im trying to compile Gaussain on a 2 Processor Opteron system > > running Suse 9.3. > > > > I have a copy of the source code for version C.02, although > > the gaussian website says that this version is compatiable > > with SUSE 9.3, the htm file on the CDROM only mentions up to > > Suse 9.1. Is this a problem ? > > > > I have installed the kernal patch as suggested on the > > Gaussian Website for SUSE 9.3. > > > > The guassian installation goes smoothly until i run the > > g03.login script i get the message that gau-machine does not > > exist. Is this a problem ? When u try and compile G03 this > > file is created and it returns the message AMD-64. > > > > When you try and run the compile script, it does not even > > manage to successfully compile the .c files such as fslipt.c > > it gives a error message of > > > > cc1: error: CPU you selected does not support x86-64 instruction set > > cc1: error: CPU you selected does not support x86-64 instruction set > > cc1: error: -malign-double makes no sense in the 64bit mode > > > > I had similar problems when compiling MOPAC, i removed the > > -malign-double switch which sorted them. I believe the first > > 2 errors are caused by the -march=i48 switch. I can not find > > where to these switches are declared in the script however. > > > > The script does not managed to get near to compiling the > > fortran files. I currently have downloaded the trial of the > > portland group fortran compilier 6.0. I have changed some of > > the g03.login script to point to version 6.0 instead of 5.1. > > I am using the demo version just to get to grips with > > compiling guassian. > > > > However we have a copy of the lastest verion of Intel Fortran > > compilier does any one know if it would be possible to > > compile Gaussian on an Opteron system using this compiler ? > > > > Thanks for any help > > > > Roger > > > > > > > > -= This is automatically added to each message by the mailing > > script =- To recover the email address of the author of the > > message, please change the strange characters on the top line > > to the (0) sign. You can also look up the X-Original-From: line > > in the mail header.> > > Search Messages: http://www.ccl.net/htdig (login: ccl, > > Password: search)> > > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ > > -+-+-+-+-+> > > -- Jozsef Csontos, Ph.D. Department of Biomedical Sciences Creighton University, Omaha, NE From owner-chemistry@ccl.net Fri Dec 9 14:39:00 2005 From: "Himanshu Khandelia hkhandel a dtc.umn.edu" To: CCL Subject: CCL: molecular modeling - animation Message-Id: <-30255-051209115904-2068-K6On1L9veuAbMNKbMh3bNw!^!server.ccl.net> X-Original-From: Himanshu Khandelia Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 9 Dec 2005 10:58:58 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: Himanshu Khandelia [hkhandel**dtc.umn.edu] I think the best tool is to use VMD. Just open the pdb, and the dcd, and use the vmdmovie command in the extensions menu. VMD will come up with a nice mpeg for you. Works better on linux than windows in my opinion =================================================== Himanshu Khandelia Doctoral Candidate, Kaznessis Research, Department of Chemical Engineering and Materials Science, University of Minnesota Mailing Address: 499, Walter Library, 117, Pleasant St. SE, Minneapolis, MN 55455 Phone(o): 612-624-4945 =================================================== On Fri, 9 Dec 2005, Jason Gans jgans*lanl.gov wrote: > Sent to CCL by: Jason Gans [jgans{:}lanl.gov] > Qmol (windows only, http://www.mbg.cornell.edu/Shalloway_Lab_QMOL.cfm) > will make movies using a PDB and a DCD file or a PDB file will multiple > structures. > > Regards, > > Jason > > On Dec 8, 2005, at 1:50 PM, ramesh r ramesh_ass]_[yahoo.co.in wrote: > > > Sent to CCL by: ramesh r [ramesh_ass : yahoo.co.in] > > --0-41187699-1134060055=:97686 > > Content-Type: text/plain; charset=iso-8859-1 > > Content-Transfer-Encoding: 8bit > > > > Hi CCLers, > > I have two questions to ask related to how to create a animation and > > movie: > > 1. I may want to create a animation of a molecular model protein > > like rotation, translation and save it as file. > > 2. I have a docked complexes contains ligands and proteins. With > > this, I may want to create a movie showing docking of a ligand into > > the active site and save it in file. > > > > At this point, Could you please suggest any program do that task. > > > > Thanks in advance > > sincerely, > > ramesh> > > From owner-chemistry@ccl.net Fri Dec 9 15:14:01 2005 From: "Isaac Bersuker bersuker%x%mail.cm.utexas.edu" To: CCL Subject: CCL: [CCL] Re: CCL: crystal field & ligand field theory & MO theory Message-Id: <-30256-051209122437-9003-cMw7IeFldX/VvJnlzQbL5w---server.ccl.net> X-Original-From: Isaac Bersuker Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Fri, 09 Dec 2005 11:24:42 -0600 MIME-Version: 1.0 Sent to CCL by: Isaac Bersuker [bersuker[]mail.cm.utexas.edu] Dr Burger, The Crystal Field Theory is an approximation, sometimes a very rough approximation, while MO takes into account also covalency, so the discrepancy is not unexpected. In your case you may have also a pseudo Jahn-Teller mixing of the b2g and eg levels...Consult my book of 1996 (Wiley) for further details, if necessary. Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker() cm.utexas.edu http://www.cm.utexas.edu/directory/isaac_bersuker/ Dr. Isaac B. Bersuker Institute for Theoretical Chemistry The University of Texas at Austin Chem & Biochem Department 1 University Station A5300 Austin, TX 78712-0165 Phone: (512) 471-4671; Fax: (512) 471-8696 E-mail: bersuker() cm.utexas.edu http://www.cm.utexas.edu/directory/isaac_bersuker/ Peter Burger chburger**aci.unizh.ch wrote: >Sent to CCL by: "Peter Burger" [chburger . aci.unizh.ch] >Dear CCLers > >recently I faced a problem while teaching, i.e. > >the discrepancy of ligand field splitting and qualitative >MO theory for e.g. d8-configured square planar complexes ML4 with pure >sigma donors, e.g. [PdH4]2- (D4h symmetry). > >Is there any way to bridge the gap between the square planar ligand field splitting shown in every textbook (order dxz, dyz, then dxy or dz2 followed by dx2-y2)) and MO theory? > >The qualitiative MO (first order pertubation) treatment leaves the obviously symmetrically non-degenerate dxy (b2g) and dxz and dyz (eg) at albeit nevertheless _energetically_ identical orbital energies (all three are non-bonding in the absence of pi-acceptors). > >Is there a good way to get out of this while teaching qualitative >MO theory? The obvious problem is that students have memorized the ligand field splitting in previous lectures. > >Best regards > >Peter> > > > From owner-chemistry@ccl.net Fri Dec 9 15:49:00 2005 From: "Himanshu Khandelia hkhandel:+:dtc.umn.edu" To: CCL Subject: CCL: Linux Cluster Building Workshops Message-Id: <-30257-051209095434-13123-4WsU4UxCjX2QjprIVdbniA_-_server.ccl.net> X-Original-From: Himanshu Khandelia Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Fri, 9 Dec 2005 08:16:03 -0600 (CST) MIME-Version: 1.0 Sent to CCL by: Himanshu Khandelia [hkhandel(~)dtc.umn.edu] Thank you for the advice, Andrew and Kenneth. I will make sure I will not go alone on the cluster building. Will involve one of the IT geeks :) Dell etc. also provide nice xeon clusters. I wonder what the costs of these are. On Fri, 9 Dec 2005, Kenneth Geisshirt kenneth],[geisshirt.dk wrote: > Sent to CCL by: Kenneth Geisshirt [kenneth=geisshirt.dk] > Andrew D. Fant fant(~)pobox.com wrote: > >> O'Reilly, whose titles are >> usually the last work for IT topics like this, has published 2 disappointing >> volumes for this as well. The first was simply Building Linux Clusters and has >> been withdrawn from the market. The follow-on "Building High-Performance Linux >> Clusters" is better, but still is less that one might help. > > I will recommend "Building Clustered Linux Systems" by Robert W. Lucke. > >> If you simply want to put together 4-8 PCs to run a single application for you >> or a single research group, I would suggest looking at Rocks ( >> http://www.rocksclusters.org) as a simple way to get something up and running. > > The Rocks distribution is easy to get going. And it's a Red Hat based > distro, many commercial software packages will be easy to install. > Moreover, the many 3rd party package repositories (atrpms.net etc.) can > be integrated and you will have access to a large code base. > >> My biggest bit of advice, however, comes from a bumper sticker that the >> electrician's union hands out around here. "Wiring Is Not A Hobby". If you are >> going to be running multiple applications from multiple sources/vendors, going >> above about 10 systems, having users from more than one fairly tight-knit and >> cooperative research group, or making the results from this cluster the basis >> of your research plans, you probably want to get an IT professional involved. > > I can second that (I'm one of those IT professionals). Linux clusters > ain't rocket science but the complexity can be huge. If you start from > scratch you have to decide which Ethernet switch is best, how to wire > the stuff (low level) and which policy to implement in your batch system > (high level). If you build a cluster every second year it's almost > impossible to keep up with the development in this area. An IT > professional might build 5-6 clusters every year so pick his brain! > > /kneth> > > -- =================================================== Himanshu Khandelia Doctoral Candidate, Kaznessis Research, Department of Chemical Engineering and Materials Science, University of Minnesota Mailing Address: 499, Walter Library, 117, Pleasant St. SE, Minneapolis, MN 55455 Phone(o): 612-624-4945 =================================================== From owner-chemistry@ccl.net Fri Dec 9 16:24:00 2005 From: "Richard Wood rwoodphd]*[msn.com" To: CCL Subject: CCL:G: A question to educational workers Message-Id: <-30258-051209124958-21014-+GhX4eaWQ3iMthEwCRFPIQ[A]server.ccl.net> X-Original-From: "Richard Wood" Content-Transfer-Encoding: 8bit Content-Type: text/plain; format=flowed; charset="iso-8859-1"; reply-type=original Date: Fri, 9 Dec 2005 12:02:43 -0500 MIME-Version: 1.0 Sent to CCL by: "Richard Wood" [rwoodphd^_^msn.com] Hi all, Here's my take on things as both a former student and also a teacher, albeit as a graduate assistant. As a student, I had no difficulty separating the model of an orbital from what was real. I think the really "good" students can grasp that concept. I think the ones that can't grasp it are the ones that aren't really interested in learning the subject because they want to, but because they have to (i.e. for an exam, or whatever reason). In teaching chemistry, my experience was that most students were "pre-med", so that was how most of them looked at chemistry, just remember the "facts" as presented, and regurgitate them on the next exam. A lot of them didn't try, or weren't inclined, to "understand" the material that was presented to them (As an aside, this reminds me of an anecdote about Richard Feynman's teaching of physics to students in Brazil during a sabbatical he took there. He would ask students to define Brewster's angle, and students could give him an almost word for word book definition; yet if he gave them the definition, or twisted his question a little bit, no one could give him the correct answer.) in such a way that they could use it. Even as a graduate student, I was shocked when given a problem on an exam, where we were asked to calculate the absorbance of a molecule using transmittance data, I was the only student that commented that the answer that I obtained based upon the numbers given in the problem was impossible, since one obtained a NEGATIVE absorbance. A related problem that I encountered in teaching chemistry, particularly at the freshman level, was the level of "math phobia" that students have/had. Here are some things that I observed in my many years as a teaching assistant: 1. Students sought a "one solution to all problems". I saw this over and over again. 2. Many students failed to put a physical meaning to the symbols in an equation, or they couldn't see when a given answer made sense or not. They also had difficulty associating values to each quantity in a given equation. 3. If you rearranged the equation, or tried to solve for a different variable, they had difficulty (see the Brewster's angle example above). 4. This was not just a "freshman" chemistry problem. I had junior and senior chem majors that had difficulty figuring out how to "make" 3 M HCl solutions starting with 6 M or 12 M stock solutions. I think that how students perceive orbitals is a moot point, as a lot of them have trouble with "simpler" problems/concepts, such as why is H2S a gas, while H2O is not, or why does HCl boil at a lower temperature than HBr. At least this is my experience. I don't think many of them know or care if orbitals are a model or are real, they are only concerned how they need to "know" about it. A question I have is this: is there any "importance" to this after one finishes their education? I mean, does the average bench chemist need to know that orbitals aren't real, but are merely mathematical models? It seems to me that most computational chemists that are working on things like drug design aren't too concerned about orbitals and whether they are real or just models. They are more interested in which interactions between a target and a ligand are important and whether a given ligand will bind to a target. I apologize in advance if I have failed to "answer" the question as posed by Dr. Sun. Just my two cents, Richard Richard L. Wood, Ph. D. Computational Chemist Cockeysville, MD 21030 rwoodphd**yahoo.com ----- Original Message ----- > From: "Roy Jensen rjensen**consol.ca" To: "Wood, Richard L. " Sent: Friday, December 09, 2005 10:10 AM Subject: CCL:G: A question to educational workers > Sent to CCL by: Roy Jensen [rjensen * consol.ca] > All > >>My current questions are directed to those who teach >>something like ["orbitals not physically real; >>orbitals not observable; objections to that orbitals >>observable"....] >> >>How do you folks explain to an average student when he >>argues with you with copies of the Nature papers, >>Science papers, C&EN news reports... that all have >>positively confirmed orbital orbservations? > > My quandary stems from the multiple definitions of 'orbital'. IUPAC > defines an orbital as the "one-electron wavefunction obtained as a > solution of the Schrödinger equation for an atom." > > Other definitions include > 1. "the space in an atom occupied by an electron, a subdivision of the > available space within an atom for an electron to orbit the nucleus" > 2. "a mathematical function used to describe the behavior of an > electron in an atom" > > Definitions that focus on the mathematical function definition > separate the orbital and the electron. Thus, THEY DO NOT CARE WHETHER > THE ORBITAL IS OCCUPIED OR NOT. > > The alternate definition asserts that THE ELECTRON IS THE ORBITAL. > Without an electron, there is no orbital. > > I am left with the following: > a) Can you observe a mathematical function? Yes. > b) Are multi-gaussian functions a reasonable MODEL for the > probability density distribution of a single electron? No. > c) Is a model real? No. > d) Is the summation of one-electron functions the same as a > multi-electron function? Only with full CI. > e) Can you observe a single electron? Not in a multi-electron > system. > f) Can you observe the sum of all the electrons in a multi-electron > system? Yes. > > I am interested in how others perceive this issue. > > Dr. Roy Jensen > (==========)-----------------------------------------¤ > Chemistry, Grant MacEwan College > Edmonton, AB T5J 4S2 > 780.633.3915 > > > > On Thu, 8 Dec 2005 17:00:23 -0500, you wrote: > >>Sent to CCL by: Sengen Sun [sengensun|yahoo.com] >>Dear college and graduate school educational workers: >> >>In the last January when we were in the hot debate, >>one of you wrote me saying something like this: >> >>["My friend, orbitals will be observed again and again >>and again..., first in Nature, then in Science, then >>in JACS, then in JPC, JOC, JIC...... The images will >>be very very pretty. I want to see by then how well >>you like those images....."] >> >>My current questions are directed to those who teach >>something like ["orbitals not physically real; >>orbitals not observable; objections to that orbitals >>observable"....] >> >>How do you folks explain to an average student when he >>argues with you with copies of the Nature papers, >>Science papers, C&EN news reports... that all have >>positively confirmed orbital orbservations? >> >>Do you have to say ["Nature papers are wrong, Science >>papers are wrong, C&EN news reports are wrong, Angew >>Chem is wrong..... Please trust me, my rationale is >>right because Hoffmann said something like orbitals >>are both real and unreal. And Hoffmann also said that >>PES tells us the ways orbitals interact..."]? >> >>Do you also have to tell the student finally that you >>cannot understand this until you drink and digest all >>deeplyu of the Pyrean (sic) spring? >> >>What else could you say? I am really curious. >> >> >>We are facing an unbearable disaster and dilemma in >>scientific education and research on this issue. This >>why I have stood up to support Dr. Eric Scerri who >>raised such an very important issue initially at CCL >>years ago. >> >> >> >>I have received a private e-mail I like the most so >>far, which says: ["You attacker are too naive if you >>think all drivers are free of alcohol"]. How wanderful >>such a metaphor! >>The quote by Hoffmann has a clear language >>word-by-word no matter how you read it. There has not >>been so far a second person who dare to say explicitly >>TRUE or FALSE to it in the public. How interesting it >>is in the modern age of human civilization in science >>and philosophy! >> >> >>Sengen >> >> >> >> >> >>__________________________________________________ >>Do You Yahoo!? >>Tired of spam? Yahoo! Mail has the best spam protection around >>http://mail.yahoo.com> > > > From owner-chemistry@ccl.net Fri Dec 9 16:59:00 2005 From: "Steve Williams willsd ~ appstate.edu" To: CCL Subject: CCL: build gamess and or ghemical on amd 64 under suse 10 linux Message-Id: <-30259-051209141325-781-IdwwST7Z5mJR9wy+WDCrRQ===server.ccl.net> X-Original-From: Steve Williams Content-transfer-encoding: 7bit Content-type: text/plain; format=flowed; charset=ISO-8859-1 Date: Fri, 09 Dec 2005 13:12:01 -0500 MIME-version: 1.0 Sent to CCL by: Steve Williams [willsd*o*appstate.edu] I have a new opteron based workstation with SuSE 10 linux installed. As a newbie to this environment (I have some, but rather limited unix experience under IRIX) I am having trouble compiling large packages. I have installed (I think) the development tools from the distribution rpms. The gcc version is 4.0.x and it does not (it seems to me) understand simple fortran. There is not (?) a compatible version of g77. There is something called gfortran with seems to compile my simple tests so they run as they should. There are several sources for the g95 rpm, but I get errors about missing media (?) when I try to install it. When I try to install ghemical, I get errors in the ./configure step, even after updating the configure script with aclocal and autoconf. I have not (so far) been able to guess enough about parameters and optimization flags to build gamess for this machine using gcc and gfortran. The portland group compiler web site has some tantalizing hints on how to do this, but of course their directions are for their compiler, not the free ones that I have now. So, I think I have a quite new system and this seems to be a problem. Has anyone built any of these applications on a system similar to mine? If so would you be willing to provide some hints on how you did so? Thanks in advance... Steve Williams From owner-chemistry@ccl.net Fri Dec 9 17:33:00 2005 From: "D.BIO- Gerard Pujadas gerard.pujadas() urv.net" To: CCL Subject: CCL: Is there non-comercial software for doing QSAR/QSAR-3D? Message-Id: <-30260-051209152854-7146-Z14ZLPry3+EE7fzEMGp6rw() server.ccl.net> X-Original-From: "D.BIO- Gerard Pujadas" Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" ; format="flowed" Date: Fri, 9 Dec 2005 20:37:36 +0100 Mime-Version: 1.0 Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas*urv.net] Dear CCL list members, I would like to know if there is non-comercial software for doing QSAR and also for doing QSAR-3D. I would also appreciate a lot your critical comments about how this non-comercial software compares with commercial ones. With many thanks in advances for your help Yours sincerely Gerard -- ======================== NOTE: NEW ADDRESS AND E-MAIL ======================== Dr. Gerard Pujadas Grup de recerca en "Vi i Salut" Dept. Bioquímica i Biotecnologia room 106 Campus de Sant Pere Sescelades e-mail: gerard.pujadas!^!urv.net Univ. Rovira i Virgili phone: 34-977 559565 C/ Marcel·lí Domingo fax: 34-977 559597 43007 Tarragona (CATALONIA) State: Spain (European Union) =========================================================================== From owner-chemistry@ccl.net Fri Dec 9 19:32:00 2005 From: "Ioana Cozmuta ioana^nas.nasa.gov" To: CCL Subject: CCL: Second Young Researchers Workshop in Mathematical Biology Message-Id: <-30261-051209161956-2786-l7JbWj9EZhG5U+EyJp+mmw###server.ccl.net> X-Original-From: "Ioana Cozmuta" Sent to CCL by: "Ioana Cozmuta" [ioana^_^nas.nasa.gov] Second Young Researchers Workshop in Mathematical Biology (March 27 - 30, 2006) Organizers: MBI postdoctoral fellows To provide a forum for young mathematical biologists to interact with their peers, the Mathematical Biosciences Institute will host the Second Young Researchers Workshop in Mathematical Biology. The workshop will bring together approximately 45 young researchers in mathematical biology to broaden their scientific perspective and to develop connections that will be important for their future careers. We cordially invite postdoctoral researchers and junior faculty to apply (http://mbi.osu.edu/forms/yrwapplyworkshop.html) for participation in this workshop. Each participant will present a poster of current research and give a 5-minute advertisement of the poster. The workshop will also feature working group discussions on broad issues relevant to researchers in mathematical biology. Plenary talks will be given by leading researchers in mathematical biology: Catherine Carr University of Maryland Leah Edelstein-Keshet University of British Columbia Bard Ermentrout University of Pittsburgh Hans Othmer University of Minnesota Timothy Secomb University of Arizona Arthur Sherman National Institutes of Health Kristin Swanson University of Washington Raimond Winslow Johns Hopkins School of Medicine Applications received by December 15, 2005 will be given full consideraton. However, applications will be accepted through December 31, 2005. There is no registration fee, and MBI will pay for local expenses. Travel support will also be available on a competitive basis. Applicants will be notified via e-mail regarding acceptance by January 31, 2006. If you have any questions, please contact Rebecca Martin at rebecca[*]mbi.osu.edu. From owner-chemistry@ccl.net Fri Dec 9 20:07:01 2005 From: "Avijit Ghosh avijit|a|physics.drexel.edu" To: CCL Subject: CCL: Orbitals and Philosophy Message-Id: <-30262-051209192655-815-wXyCtGP3xji3lkSM5J/xXA,+,server.ccl.net> X-Original-From: Avijit Ghosh Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Fri, 9 Dec 2005 18:25:08 -0500 (EST) MIME-Version: 1.0 Sent to CCL by: Avijit Ghosh [avijit{=}physics.drexel.edu] As has been pointed out any resolution to the question depends on ones definition of "orbital" as well as "real" (for instance is the word "real" being equated to the word "observable" as is used in standard QM?). W/ regards to pedagogy I think its worth emphasizing in a QM mechanics course that basis sets that one defines are orbitals are clever math tricks for solving more complicated PDEs in quantum chemistry and physics. I do however think this emphasis that hydrogenic orbitals as being "unreal" on any level before that is a mistake because regardless of where one sits on the matter, the argument hinges on subtleties of QM that are not particularly intuitive to first year undergraduates (or even graduate students and faculty like myself for that matter). That said I *personally* think orbitals are real in the same sense the multielectronic eigenstates are real for a system. That is if we neglect e-e-, interactions, we get orbitals. It seems to me that in the same sense any statement of *electronic* observables is in essense a "model" that are actually strictly non-observable due to the fact the observability in QM is based on making the born-oppenheimer approximation neglecting e-/nuclear interactions. To put it into two sentences: If we are comfortable neglecting e-e- interactions, everything becomes hydrogeneic -> hense orbitals. If we are comfortable neglecting nuclear,e- interactions ala born-oppenheimer, we can do quantum mechanics on electrons only -> hense multi-electron eigenstates and energy eigenvalues. It seems to me that either both orbitals and total electronic eigenfunctions (single quantum number valued) are both unobservable due to the approximations inherent in formulating the problem, or real with an understanding that there is a formalism of observables that is inherent to how ones defines the system and may limit the class of observables in that system (and *will change* when one defines ones system!) Incidentally, it is somewhat amusing to me that this thread actually has not only been part of the CCL list for ages, but I remember a variation of this exact thread made by many of the same players on a "philosophy of chemistry" listserv when I was a 2nd year graduate student (I think some 10 years ago at this point). _____________________________________________________________________ Avijit Ghosh, Ph.D. Drexel University, Dept of Physics Asst. Professor 3141 Chestnut st Phone: 215-895-2726 Philadelphia, PA 19104 Fax: 215-895-5934 Web: http://bio.physics.drexel.edu From owner-chemistry@ccl.net Fri Dec 9 22:01:00 2005 From: "Rajarshi Guha rxg218 : psu.edu" To: CCL Subject: CCL: Is there non-comercial software for doing QSAR/QSAR-3D? Message-Id: <-30263-051209210943-12633-U+SVJjY7jCqa4B1UKx5tBw*server.ccl.net> X-Original-From: Rajarshi Guha Content-Transfer-Encoding: 7bit Content-Type: text/plain Date: Fri, 09 Dec 2005 21:10:22 -0500 Mime-Version: 1.0 Sent to CCL by: Rajarshi Guha [rxg218|*|psu.edu] On Fri, 2005-12-09 at 17:40 -0500, D.BIO- Gerard Pujadas gerard.pujadas() urv.net wrote: > Sent to CCL by: "D.BIO- Gerard Pujadas" [gerard.pujadas*urv.net] > > Dear CCL list members, > > I would like to know if there is non-comercial > software for doing QSAR and also for doing > QSAR-3D. If we can assume that 2D QSAR consists of descriptors + statistics, for the latter you can consider the CDK or JOELib and for the latter R is a fantastic environment for the development of QSAR models and pipelines ------------------------------------------------------------------- Rajarshi Guha GPG Fingerprint: 0CCA 8EE2 2EEB 25E2 AB04 06F7 1BB9 E634 9B87 56EE ------------------------------------------------------------------- Entropy isn't what it used to be.