From chemistry-request@ccl.net Tue Feb 1 03:06:55 2005 Received: from suede.reed.edu (suede.reed.edu [134.10.2.45]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j1186rOT029206 for ; Tue, 1 Feb 2005 03:06:54 -0500 Received: from localhost (localhost.localdomain [127.0.0.1]) by suede.reed.edu (8.12.10/8.12.10) with ESMTP id j1186r3H012752 for ; Tue, 1 Feb 2005 00:06:53 -0800 Received: from suede.reed.edu ([127.0.0.1]) by localhost (smtp-1.reed.edu [127.0.0.1]) (amavisd-new, port 10024) with LMTP id 12247-09 for ; Tue, 1 Feb 2005 00:06:52 -0800 (PST) Received: from imap.reed.edu (imap.reed.edu [134.10.2.10]) by suede.reed.edu (8.12.10/8.12.10) with ESMTP id j1186pT3012740 (version=TLSv1/SSLv3 cipher=EDH-RSA-DES-CBC3-SHA bits=168 verify=NOT) for ; Tue, 1 Feb 2005 00:06:51 -0800 Received: from [127.0.0.1] (dsl-206-103-41-215.dsl.easystreet.com [206.103.41.215]) (authenticated bits=0) by imap.reed.edu (8.12.10/8.12.10) with ESMTP id j1186nmI015427 (version=TLSv1/SSLv3 cipher=RC4-MD5 bits=128 verify=NOT) for ; Tue, 1 Feb 2005 00:06:51 -0800 Message-ID: <41FF3956.6000307=at=reed.edu> Date: Tue, 01 Feb 2005 00:09:58 -0800 From: Alan Shusterman User-Agent: Mozilla Thunderbird 1.0 (Windows/20041206) X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry=at=ccl.net Subject: CCL: orbitals and reality Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-Virus-Scanned: by amavisd-new at smtp-1.reed.edu X-Spam-Status: No, hits=3.9 required=7.5 tests=MY_DSL,NO_RDNS2 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net I find the introduction of the trajectory analogy interesting, but I think it is inappropriate to equate trajectories with orbitals (maybe I misunderstood the analogy?). I would use trajectories this way: 1. let a classical trajectory be analogous to a complete wave function (not an orbital) 2. and suppose we have a complicated system so that the trajectory (like a complete wave function) cannot be expressed analytically 3. in this case, we will try to model the trajectory with a combination of simpler analytical functions, like short line segments 4. the line segments are analogous to orbitals Now we can return to the question of what can be measured. We might claim that a measurement teaches us something about the trajectory. However, it seems misguided to claim a measurement tells us the length or direction of the line segments. We only invented the line segments as a tool for approximating the trajectory. Granted, it's not a perfect analogy. But consider one more thing: as we approach the limiting situation of an infinite number of infinitely short line segments, our trajectory model does approach the actual trajectory. On the other hand, the limiting situation of an infinite number of orbitals only approaches the Hartree-Fock limit (a model) and never the actual wave function. It seems very strange to say we have measured orbitals. -Alan -- Alan Shusterman Chemistry Department Reed College Portland, OR 97202-8199 503-517-7699 http://academic.reed.edu/chemistry/alan/ "The Way you can go isn't the real Way." Lao Tzu From chemistry-request@ccl.net Tue Feb 1 06:05:43 2005 Received: from postfix3-2.free.fr (postfix3-2.free.fr [213.228.0.169]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j11B5era005504 for ; Tue, 1 Feb 2005 06:05:40 -0500 Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-2.free.fr (Postfix) with ESMTP id 1681DC213; Tue, 1 Feb 2005 12:05:38 +0100 (CET) In-Reply-To: References: Mime-Version: 1.0 (Apple Message framework v619.2) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <4ce7535b5e7449995f7e1aa1e6083c60 -()- cea.fr> Content-Transfer-Encoding: 7bit Cc: CCL From: khinsen -()- cea.fr Subject: Re: CCL:orbitals and reality Date: Tue, 1 Feb 2005 12:05:39 +0100 To: Eric Scerri X-Mailer: Apple Mail (2.619.2) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 01.02.2005, at 00:14, Eric Scerri wrote: > Many useful things are unobservable! > > The question was indeed whether one can observe an orbital. > I don't think anybody really doubts the usefulness of the concept. > > Electrons and nuclei are at least observable in principle. > The usual understanding is that orbitals are not. Electrons and nuclei are not observable, its some of their properties that are. The position, velocity, energy, charge, etc. of an electron are observables. Other properties, such as its wave function, are not observables. When we say "electrons are observable", this is really just a shorthand for saying "electrons have observable properties". Note also that the status of a quantity as an "observable" is part of the model, not of "reality". The model of an electron with all the properties listed in physics textbooks is the outcome of a long process of experimentation and model making. There is no operation that allows to establish the list of all observable properties of an electron. They might become more numerous in the future, but future research might also lead us to abandon the concept of the electron, or at least downgrade its status in our understanding of nature. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen -()- cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Tue Feb 1 08:41:51 2005 Received: from sender-01.it.helsinki.fi (sender-01.it.helsinki.fi [128.214.205.139]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j11Dfnra013364 for ; Tue, 1 Feb 2005 08:41:50 -0500 Received: from heavy.it.helsinki.fi (heavy.it.helsinki.fi [128.214.189.109]) by sender-01.it.helsinki.fi (8.13.3/8.13.3) with ESMTP id j11C7K15014297; Tue, 1 Feb 2005 14:07:20 +0200 Received: from heavy.it.helsinki.fi (localhost [127.0.0.1]) by heavy.it.helsinki.fi (8.12.10/8.12.10) with ESMTP id j11C7K3h429570; Tue, 1 Feb 2005 14:07:20 +0200 (EET) Received: from localhost (sundius@localhost) by heavy.it.helsinki.fi (8.12.10/8.12.10/Submit) with ESMTP id j11C7KOP429601; Tue, 1 Feb 2005 14:07:20 +0200 (EET) X-Authentication-Warning: heavy.it.helsinki.fi: sundius owned process doing -bs Date: Tue, 1 Feb 2005 14:07:19 +0200 (EET) From: Tom Sundius X-X-Sender: sundius^at^heavy.it.helsinki.fi To: khinsen^at^cea.fr cc: Eric Scerri , CCL Subject: Re: CCL:orbitals and reality In-Reply-To: <4ce7535b5e7449995f7e1aa1e6083c60^at^cea.fr> Message-ID: References: <4ce7535b5e7449995f7e1aa1e6083c60^at^cea.fr> MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On Tue, 1 Feb 2005 khinsen^at^cea.fr wrote: > On 01.02.2005, at 00:14, Eric Scerri wrote: > >> Many useful things are unobservable! >> >> The question was indeed whether one can observe an orbital. >> I don't think anybody really doubts the usefulness of the concept. >> >> Electrons and nuclei are at least observable in principle. >> The usual understanding is that orbitals are not. > > Electrons and nuclei are not observable, its some of their properties that > are. The position, velocity, energy, charge, etc. of an electron are > observables. Other properties, such as its wave function, are not > observables. When we say "electrons are observable", this is really just a > shorthand for saying "electrons have observable properties". ... I agree completely. I would also like to add that you have to take Heisenberg's uncertainty relation into account. Thus the motion of electrons and nuclei cannot be compared to the classical motion of "balls in flight", as was suggested earlier in this discussion. The quantum world is very different from the "classical world", that is why it is not possible directly to "observe" a wave function. Tom Sundius University of Helsinki, Dept of Physical Sciences phone +358-9-191 50672 P.O.Box 64, FIN-00014 Helsinki, Finland fax +358-9-191 50610 +++ for we know in part, and we prophesy in part +++ From chemistry-request@ccl.net Tue Feb 1 08:52:16 2005 Received: from mailhub130.itcs.purdue.edu (mailhub130.itcs.purdue.edu [128.210.5.130]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j11DqEra013946 for ; Tue, 1 Feb 2005 08:52:15 -0500 Received: from [128.46.108.125] (frny117bpc05.ecn.purdue.edu [128.46.108.125]) by mailhub130.itcs.purdue.edu (8.13.1/8.13.1/avscan-smtp) with ESMTP id j11DqEBV021311; Tue, 1 Feb 2005 08:52:14 -0500 Message-ID: <41FF8990.8010304 %a% purdue.edu> Date: Tue, 01 Feb 2005 08:52:16 -0500 From: Aaron Deskins User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en MIME-Version: 1.0 To: khinsen %a% cea.fr CC: CCL Subject: Re: CCL:orbitals and reality References: <4ce7535b5e7449995f7e1aa1e6083c60 %a% cea.fr> In-Reply-To: <4ce7535b5e7449995f7e1aa1e6083c60 %a% cea.fr> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit X-PMX-Version: 4.7.0.111621 X-PerlMx-Virus-Scanned: Yes X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Not to be too pedantic, but what is an example of an observable? When we say we observe something, are we not just observing its properties? For example I may say, "I see a red book." Actually I'm only observing its properties. The book has the properties of interacting with visible light to make it appear red. I've only observed its light-related properties. If I touch the book, I have observed its mass-related properties. Are not all observables based on its properties? khinsen %a% cea.fr wrote: > > Electrons and nuclei are not observable, its some of their properties > that are. The position, velocity, energy, charge, etc. of an electron > are observables. Other properties, such as its wave function, are not > observables. When we say "electrons are observable", this is really > just a shorthand for saying "electrons have observable properties". > > Note also that the status of a quantity as an "observable" is part of > the model, not of "reality". The model of an electron with all the > properties listed in physics textbooks is the outcome of a long > process of experimentation and model making. There is no operation > that allows to establish the list of all observable properties of an > electron. They might become more numerous in the future, but future > research might also lead us to abandon the concept of the electron, > or at least downgrade its status in our understanding of nature. > -- From chemistry-request@ccl.net Tue Feb 1 09:52:36 2005 Received: from postfix3-2.free.fr (postfix3-2.free.fr [213.228.0.169]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j11EqXra017864 for ; Tue, 1 Feb 2005 09:52:33 -0500 Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-2.free.fr (Postfix) with ESMTP id 12B7DC283; Tue, 1 Feb 2005 15:52:32 +0100 (CET) In-Reply-To: <41FF8990.8010304_at_purdue.edu> References: <4ce7535b5e7449995f7e1aa1e6083c60_at_cea.fr> <41FF8990.8010304_at_purdue.edu> Mime-Version: 1.0 (Apple Message framework v619.2) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <43b31c26646dfac0609eabbe4a42a3ad_at_cea.fr> Content-Transfer-Encoding: 7bit Cc: CCL From: khinsen_at_cea.fr Subject: Re: CCL:orbitals and reality Date: Tue, 1 Feb 2005 15:52:31 +0100 To: Aaron Deskins X-Mailer: Apple Mail (2.619.2) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 01.02.2005, at 14:52, Aaron Deskins wrote: > Not to be too pedantic, but what is an example of an observable? When > we I was using that term in the technical sense of quantum theory, i.e. a quantity represented by a Hermitian operator. The position of an electron for example. > example I may say, "I see a red book." Actually I'm only observing its > properties. The book has the properties of interacting with visible > light to make it appear red. I've only observed its light-related > properties. If I touch the book, I have observed its mass-related > properties. Are not all observables based on its properties? That's exactly what I wanted to say in my post as well! -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen_at_cea.fr ------------------------------------------------------------------------ ------- From chemistry-request@ccl.net Tue Feb 1 02:03:07 2005 Received: from smtp1.Stanford.EDU (smtp1.Stanford.EDU [171.67.16.123]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j11735OT027062 for ; Tue, 1 Feb 2005 02:03:06 -0500 Received: from cardinal1.Stanford.EDU (cardinal1.Stanford.EDU [171.64.15.249]) by smtp1.Stanford.EDU (8.12.11/8.12.11) with ESMTP id j115svM5010930 for ; Mon, 31 Jan 2005 21:54:58 -0800 Date: Mon, 31 Jan 2005 21:54:57 -0800 (PST) From: "S.I.Gorelsky" To: Computational Chemistry List Subject: orbital interaction diagrams In-Reply-To: <200502010218.j112IJT9008167 ^^^ electra.cc.umanitoba.ca> Message-ID: MIME-Version: 1.0 Content-Type: TEXT/PLAIN; charset=US-ASCII X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Speaking of orbitals and useful constructs... The new version of AOMix-CDA is available for downloading. The new version allows you to analyze the orbital interactions between molecular fragments in all spin coupling cases (ferromagnetic and anti-ferromagnetic). For more details and examples, please go to http://www.sg-chem.net/aomix-s/ With best regards, S.G. ---------------------------------------------------------------- Dr S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Phone: (650) 723-0041. Fax: (650) 723-0852. ---------------------------------------------------------------- From chemistry-request@ccl.net Tue Feb 1 03:54:38 2005 Received: from smtp.bii-sg.org (nfs1000.bii.a-star.edu.sg [202.6.243.8]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j118sYOT031334 for ; Tue, 1 Feb 2005 03:54:36 -0500 Received: (qmail 8381 invoked from network); 1 Feb 2005 08:54:28 -0000 Received: from unknown (HELO ?10.217.5.82?) (chandra@10.217.5.82) by apps5.bii.a-star.edu.sg with SMTP; 1 Feb 2005 08:54:28 -0000 Message-ID: <41FF433C.8010409 |a| bii.a-star.edu.sg> Date: Tue, 01 Feb 2005 16:52:12 +0800 From: Chandra User-Agent: Mozilla/5.0 (Windows; U; Windows NT 5.1; en-US; rv:1.7.2) Gecko/20040803 X-Accept-Language: en-us, en MIME-Version: 1.0 To: chemistry |a| ccl.net Subject: Water Content-Type: text/plain; charset=us-ascii; format=flowed Content-Transfer-Encoding: 7bit X-Spam-Status: No, hits=0.0 required=7.5 tests=none autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Does anyone have a reference to computations of entropies (quasiharmonic) of liquid water from MD simulations with the various water models such as TIP3, SPC etc. many thanks chandra From chemistry-request@ccl.net Tue Feb 1 04:44:47 2005 Received: from up.univ-mrs.fr (mailup.univ-mrs.fr [147.94.113.16]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j119ikra001856 for ; Tue, 1 Feb 2005 04:44:46 -0500 Received: from localhost (localhost [127.0.0.1]) by up.univ-mrs.fr (Postfix) with ESMTP id B5AD713BE77 for ; Tue, 1 Feb 2005 10:44:45 +0100 (CET) Received: from up.univ-mrs.fr ([127.0.0.1]) by localhost (mailup.univ-mrs.fr [127.0.0.1]) (amavisd-new, port 10024) with ESMTP id 145746-04 for ; Tue, 1 Feb 2005 10:44:45 +0100 (CET) Received: from [147.94.185.160] (unknown [147.94.185.160]) by up.univ-mrs.fr (Postfix) with ESMTP id 05F6517D306 for ; Tue, 1 Feb 2005 10:44:45 +0100 (CET) Message-ID: <41FF4F95.9000803 = = = up.univ-mrs.fr> Date: Tue, 01 Feb 2005 10:44:53 +0100 From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Organization: LCTMM User-Agent: Mozilla/5.0 (X11; U; Linux i686; fr-FR; rv:1.7.2) Gecko/20040804 X-Accept-Language: fr-fr, en-us, en MIME-Version: 1.0 To: chemistry = = = ccl.net Subject: Re: CCL:orbitals and reality References: <41FF3956.6000307 = = = reed.edu> In-Reply-To: <41FF3956.6000307 = = = reed.edu> X-Enigmail-Version: 0.85.0.0 X-Enigmail-Supports: pgp-inline, pgp-mime Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit X-Virus-Scanned: by amavisd-new at up.univ-mrs.fr X-Spam-Status: No, hits=4.0 required=7.5 tests=NO_RDNS,NO_RDNS2,RM_ft_Iso8859 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net Hum ... I only said 1-e orbitals and trajectories are analog as human mind creations ! Useful but not measurable. In Hartree-Fock theory, a two-electrons system can be *approximately* described by some linear combinations of one-electron orbitals. But the correlation lacks. In classical mechanics, the combined trajectories of two interacting objects can be written as the sum of the trajectories f(r_i) of each individual object, but some physics also lack: collisions between the two objects for instance. In this case, we need to add an explicit dependance of f in r_i and r_ij. That means that looking at one individual classical trajectory in a two-objects system is meaningless if we are interested in describing the whole behavior of the system. In the same way, any QC theory based on 1-electron functions is an approximate theory, helpful but always lacking some features ! Now, can these 1-electron functions capture *some* physics of what is the behavior of a single electron in the field of some other particles ? Some, certainly. But does it mean we can measure them ? I don't think so, even less than the true full wavefunction that describes the simultaneous behavior of all the interacting particles. Alan Shusterman a icrit : > I find the introduction of the trajectory analogy interesting, but I > think it is inappropriate to equate trajectories with orbitals (maybe I > misunderstood the analogy?). > > I would use trajectories this way: > 1. let a classical trajectory be analogous to a complete wave function > (not an orbital) > 2. and suppose we have a complicated system so that the trajectory (like > a complete wave function) cannot be expressed analytically > 3. in this case, we will try to model the trajectory with a combination > of simpler analytical functions, like short line segments > 4. the line segments are analogous to orbitals > > Now we can return to the question of what can be measured. We might > claim that a measurement teaches us something about the trajectory. > However, it seems misguided to claim a measurement tells us the length > or direction of the line segments. We only invented the line segments as > a tool for approximating the trajectory. > > Granted, it's not a perfect analogy. But consider one more thing: as we > approach the limiting situation of an infinite number of infinitely > short line segments, our trajectory model does approach the actual > trajectory. On the other hand, the limiting situation of an infinite > number of orbitals only approaches the Hartree-Fock limit (a model) and > never the actual wave function. It seems very strange to say we have > measured orbitals. > > -Alan > -- Dr. Nicolas Ferre' Laboratoire de Chimie Theorique et de Modelisation Moleculaire UMR 6517 - CNRS Universite' de Provence Case 521 - Faculte' de Saint-Jerome Av. Esc. Normandie Niemen 13397 MARSEILLE Cedex 20 (FRANCE) Tel : (+33)4.91.28.27.33 Fax : (+33)4.91.28.87.58 Please avoid sending me Word or PowerPoint attachments. See http://www.gnu.org/philosophy/no-word-attachments.html From chemistry-request@ccl.net Tue Feb 1 11:18:14 2005 Received: from web50401.mail.yahoo.com (web50401.mail.yahoo.com [206.190.38.66]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j11GIAra021674 for ; Tue, 1 Feb 2005 11:18:11 -0500 Received: (qmail 60949 invoked by uid 60001); 1 Feb 2005 15:18:09 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=GwASl+4FcyI3ARpUs1vNbhsY+jqnMd9rccRjmtPBZebX/UOtzDSrpJhd99FqHAvQd55Wk0vDvb/ODxXmP5wY6VZYZF7QBXgJnEqY80NOlPuCdIM/FMKcm/wSuulzMTgBnDWN18hXu29LpS+5iIcGzPgN2rEUiN94cWfdKdK5nfM= ; Message-ID: <20050201151809.60947.qmail |a| web50401.mail.yahoo.com> Received: from [193.179.225.19] by web50401.mail.yahoo.com via HTTP; Tue, 01 Feb 2005 07:18:09 PST Date: Tue, 1 Feb 2005 07:18:09 -0800 (PST) From: Bruno Sopko Subject: Re: CCL:set stack size with ulimit under OS X 10.3 To: Kenneth Overly , CHEMISTRY |a| ccl.net In-Reply-To: MIME-Version: 1.0 Content-Type: multipart/alternative; boundary="0-669528859-1107271089=:60908" X-Spam-Status: No, hits=3.4 required=7.5 tests=HTML_MESSAGE,MK_BAD_HTML_04, MK_YAHOO_REDIR_01,MY_MANY_BR,WLS_URI_OPT_150 autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net --0-669528859-1107271089=:60908 Content-Type: text/plain; charset=us-ascii I am no expert in OS X, but I suppose that you will need to modify (or create) file named for instance autodock.sh in your /etc/init.d directory (or from where the startup - shutdown files are read, that is the part of OS X, I do not remeber). This should solve your problem. The other possibility is to recompile the autodock with -stack, 86089 switch. Hope this will help Brun Sopko Kenneth Overly wrote: I'm trying to run AutoDock on a dual 2 GHz G5 running OS X 10.3. Fortunately, the folks at Scripps have provided precompiled binaries of AutoDock and AutoGrid for OS X. My problem is setting the stack size to unlimited under OS X. Like Linux, OS X uses a bashrc file for systemwide bash configuration. I can edit the file to add "ulimit -s unlimited" as superuser (using sudo) but OS X won't allow my default account (which has administrator privileges) to modify the stack size. I'm pretty sure this has something to do with the peculiarities of OS X but I'm not sure how to fix it. Can anyone shed some light? -- Kenneth R. Overly, Ph.D., Assoc. Prof. of Chemistry Providence College Dept. of Chemistry and Biochemistry Providence, RI 02918 -= 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 |a| ccl.net Send your subscription/unsubscription requests to: CHEMISTRY-REQUEST |a| 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, jlabanow |a| nd.edu (read about it on CCL Home Page) -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+ --------------------------------- Do you Yahoo!? Yahoo! Search presents - Jib Jab's 'Second Term' --0-669528859-1107271089=:60908 Content-Type: text/html; charset=us-ascii
I am no expert in OS X, but I suppose that you will need to modify (or create) file named
for instance autodock.sh in your /etc/init.d directory (or from where the startup - shutdown files are read, that is the part of OS X, I do not remeber). This should solve your problem. The other possibility is to recompile the autodock with -stack, 86089 switch.
 
Hope this will help
 
Brun Sopko

Kenneth Overly <koverly |a| providence.edu> wrote:
I'm trying to run AutoDock on a dual 2 GHz G5 running OS X 10.3.
Fortunately, the folks at Scripps have provided precompiled binaries of
AutoDock and AutoGrid for OS X. My problem is setting the stack size to
unlimited under OS X. Like Linux, OS X uses a bashrc file for systemwide
bash configuration. I can edit the file to add "ulimit -s unlimited" as
superuser (using sudo) but OS X won't allow my default account (which has
administrator privileges) to modify the stack size. I'm pretty sure this has
something to do with the peculiarities of OS X but I'm not sure how to fix
it. Can anyone shed some light?
--
Kenneth R. Overly, Ph.D., Assoc. Prof. of Chemistry
Providence College
Dept. of Chemistry and Biochemistry
Providence, RI 02918



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Yahoo! Search presents - Jib Jab's 'Second Term' --0-669528859-1107271089=:60908-- From chemistry-request@ccl.net Tue Feb 1 11:30:06 2005 Received: from web30801.mail.mud.yahoo.com (web30801.mail.mud.yahoo.com [68.142.200.144]) by server.ccl.net (8.12.8/8.12.8) with SMTP id j11GU5ra022218 for ; Tue, 1 Feb 2005 11:30:05 -0500 Received: (qmail 60366 invoked by uid 60001); 1 Feb 2005 16:12:16 -0000 Comment: DomainKeys? See http://antispam.yahoo.com/domainkeys DomainKey-Signature: a=rsa-sha1; q=dns; c=nofws; s=s1024; d=yahoo.com; b=VtXubgg8D9qKcEM2xFlD4YdjHetdpjLItSiS370lxLF5PsEySiVyG9LowNX5lmTye7SaizwpAjC5/HoZ+167lp2GJLu/xf2sD7eL/LNyu3LY4MaTk6LLmu4ZK4kkx4lty0Nf8S50rGZ2S5ocshU+TULau9Se7qUNGc0Renzz1+E= ; Message-ID: <20050201161216.60364.qmail !v! web30801.mail.mud.yahoo.com> Received: from [67.110.18.100] by web30801.mail.mud.yahoo.com via HTTP; Tue, 01 Feb 2005 08:12:16 PST Date: Tue, 1 Feb 2005 08:12:16 -0800 (PST) From: Guosheng Wu Subject: Re: CCL:orbitals and reality To: Tom Sundius , khinsen !v! cea.fr Cc: Eric Scerri , CCL In-Reply-To: MIME-Version: 1.0 Content-Type: text/plain; charset=us-ascii X-Spam-Status: No, hits=3.5 required=7.5 tests=FORGED_YAHOO_RCVD, FROM_ENDS_IN_NUMS,FROM_HAS_ULINE_NUMS autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net > >> Many useful things are unobservable! > >> > >> The question was indeed whether one can observe an orbital. > >> I don't think anybody really doubts the usefulness of the concept. > >> > >> Electrons and nuclei are at least observable in principle. > >> The usual understanding is that orbitals are not. > > > > Electrons and nuclei are not observable, its some of their properties > > that are. The position, velocity, energy, charge, etc. of an electron >> are observables. Other properties, such as its wave function, are not > > observables. >> When we say "electrons are observable", this is really > just a shorthand for saying "electrons have observable properties". > >... The last statement should also be true for wave function?! And that Nature paper did observe some properties of the wave function of N2. Of course we know QM is different from CM, but what is the difference between the wave of electron and the wave of light? In some sense the exact solution of wave function for a molecule of course has very meaningful property of the system, such as H atom, harmonic vibrator,... do not bother me with complicated molecules! In principle that's the same thing, please forget about multi-electron system for a second, NOW some folks are talking about any kind of wave function! As I mentioned last time, exact solution of wave function is the probability amplititude, it is not <>, it's very meaningful stuff. Certainly b/c the nature of QM especially the principle of uncertainty, it's absolute value may not mean much, especially when it's a complex function, but things like |psi|, or just psi itself when it's real like H atom, or , (density) or ,.... each one is meaningful, and observable for simple systems! I guess in the future experiments would definitely provide better answers to some of the listers, and it's the advantage of experiment that might be able to provide useful and meaningful tool to help the validataion of QM theories for complicated system, where the exact solution of SE is terribly difficult. It might be better for us to check some graduate-level Quantum mechanics book carefully, not Quantum chemistry book, definitely not any kind of book like quantum organic chemistry, if there may be any. BTW, can not we find something more meaningful to discuss instead of this "Orbitals and reality"? Thanks for reading. -Guosheng Wu __________________________________ Do you Yahoo!? Yahoo! Mail - You care about security. So do we. http://promotions.yahoo.com/new_mail From chemistry-request@ccl.net Tue Feb 1 12:12:44 2005 Received: from postfix3-2.free.fr (postfix3-2.free.fr [213.228.0.169]) by server.ccl.net (8.12.8/8.12.8) with ESMTP id j11HCgra024226 for ; Tue, 1 Feb 2005 12:12:42 -0500 Received: from [82.66.102.10] (michelet-4-82-66-102-10.fbx.proxad.net [82.66.102.10]) by postfix3-2.free.fr (Postfix) with ESMTP id 86C7CC39B; Tue, 1 Feb 2005 18:12:40 +0100 (CET) In-Reply-To: <20050201161216.60364.qmail)at(web30801.mail.mud.yahoo.com> References: <20050201161216.60364.qmail)at(web30801.mail.mud.yahoo.com> Mime-Version: 1.0 (Apple Message framework v619.2) Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Message-Id: <7ba2491acf8060fe09bc21f2f43f30ea)at(cea.fr> Content-Transfer-Encoding: 7bit Cc: CCL list (E-mail) From: khinsen)at(cea.fr Subject: Re: CCL:orbitals and reality Date: Tue, 1 Feb 2005 18:12:37 +0100 To: Guosheng Wu X-Mailer: Apple Mail (2.619.2) X-Spam-Status: No, hits=1.0 required=7.5 tests=NO_REAL_NAME autolearn=no version=2.61 X-Spam-Checker-Version: SpamAssassin 2.61 (1.212.2.1-2003-12-09-exp) on servernd.ccl.net On 01.02.2005, at 17:12, Guosheng Wu wrote: >> When we say "electrons are observable", this is really >> just a shorthand for saying "electrons have observable properties". >> ... > > The last statement should also be true for wave function?! And that Before introducing linguistic shorthands about observable aspects of wavefunctions, we'd better make sure we understand and agree on all those aspects! > Nature paper did observe some properties of the wave function of N2. Fine, but that's something entirely different from what I described before. I used "observable" as a technical term from quantum theory, i.e. a quantity represented by a Hermitian operator. This is not the same as the common language meaning of "something that can be observed". The latter is quite vague as it can apply to both objects ("a brick is observable") and properties (the colour of a brick is observable") and leaves the notion of "observation" open to interpretation (and this is a tricky one in quantum theory). > Of course we know QM is different from CM, but what is the difference > between the wave of electron and the wave of light? In some sense the The nature of the field associated with the wave. In the case of light, it's the electric and magnetic field, which are observables (in quantum field theory). In the case of a wave function of an electron, it is a non-observable quantity (again within the framework of quantum theory). > much, especially when it's a complex function, but things like |psi|, > or > just psi itself when it's real like H atom, or , > (density) or ,.... each one is meaningful, and observable > for > simple systems! I guess in the future experiments would definitely Obviously many quantities derived from the wave function can be obtained experimentally. But that is not the same as observing the wave function itself. -- ------------------------------------------------------------------------ ------- Konrad Hinsen Laboratoire Leon Brillouin, CEA Saclay, 91191 Gif-sur-Yvette Cedex, France Tel.: +33-1 69 08 79 25 Fax: +33-1 69 08 82 61 E-Mail: khinsen)at(cea.fr ------------------------------------------------------------------------ -------