From owner-chemistry@ccl.net Sun Feb 19 13:04:00 2006 From: "Ross Walker ross~!~rosswalker.co.uk" To: CCL Subject: CCL: Help on Molecular Dynamics software Message-Id: <-30926-060218160007-19436-wXyCtGP3xji3lkSM5J/xXA__server.ccl.net> X-Original-From: "Ross Walker" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="US-ASCII" Date: Sat, 18 Feb 2006 11:44:09 -0800 MIME-Version: 1.0 Sent to CCL by: "Ross Walker" [ross|,|rosswalker.co.uk] Dear Hao, > Does anyone know a good parallel Molecular Dynamics code that > can handle polarizable force field such as Dang-Chang or > AMOEBA? I am currently using TINKER, which is a very good > package, but the code is not paralleled. Amber v9 which is currently scheduled for release at the end of March will have support for parallel simulations using the Ameoba force field. Details will be available here once the release date is firm. (http://amber.scripps.edu) All the best Ross /\ \/ |\oss Walker | Department of Molecular Biology TPC15 | | The Scripps Research Institute | | Tel: +1 858 784 8889 | EMail:- ross,,rosswalker.co.uk | | http://www.rosswalker.co.uk | PGP Key available on request | Note: Electronic Mail is not secure, has no guarantee of delivery, may not be read every day, and should not be used for urgent or sensitive issues. From owner-chemistry@ccl.net Sun Feb 19 19:04:00 2006 From: "Sengen Sun sengensun^-^yahoo.com" To: CCL Subject: CCL: Lowdin and Mulliken population Message-Id: <-30927-060219185926-17759-cFox/nN+05qBKgDGIayMmg _ server.ccl.net> X-Original-From: Sengen Sun Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Sun, 19 Feb 2006 15:59:18 -0800 (PST) MIME-Version: 1.0 Sent to CCL by: Sengen Sun [sengensun%x%yahoo.com] I still wish to emphasize that the use of Mulliken and natural charges should not be banned! They are the most popular parameters embodied in almost any common software packages such as Spartan. I also knew well Bader's treasure - AIM. And I do think that Bader and his work have not been given enough respect they actually deserve. But I insist that my use of M-charges in my work be justified. I think that I have made a breakthrough in the fundamental understanding of concerted cycloadditions. If my theory is correct, every chemist (either experimental or theoretical) and every student in chemistry should be able to verify the theory personally using a commercially available and cheap softwre package such as Spartan. It was my intention to create such a sitting in my papers. There are always two kinds of things - high quality of high price and low quality of low price. It is often not necessary to pay a high price to reach a goal. Theoretical organic chemistry is about understanding of chemical concepts. One may use any satisfactory mathematical tool at his/her convenience. Again, James Robinson is right. In addition, this discussion provides me a good opportunity to discuss my mechanistic theory further. In the last week, four people wrote me and asked for my preprint papers. Now I have uploaded to the CCL site one of the papers and a ppt presentation I used twice in 2005 for two international symposiums. The paper was the first paper I posted in the Chemistry Preprint Server 5 years ago. Many people already have it. http://server.ccl.net/cca/documents/ConcertedCycloadditons/ http://server.ccl.net/cca/documents/ConcertedCycloadditons_2/ I thank some CCLers who urged me to publish my research work professionally. I have never given up my effort doing so for more than 7 years. I apologize to the people who don't like my posts, but please use the web tool to block my posts. My findings on the theoretical knowledge of concerted cycloadditions are based on such a "ridiculously" simple method that it is simply ridiculous to some people. I evaluated some arbitrary colliding complexes and learned some new and very important knowledge that is valid in understanding the concerted pathway. I formulated some new and interesting concepts such as conjugation hindrances and easiness of electronic migration that decide organic chemical reactivity. I invite every one to criticize my theory on a scientific basis. I invite you to defeat my sensational claims I made in the Conclusions of my ppt presentation. If I am convinced anything I made wrong, I will correct or withdraw it. I am patient and determined to learn something by engaging in the Internet discusions. Thanks to every one. Sengen __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com From owner-chemistry@ccl.net Sun Feb 19 19:38:00 2006 From: "Lukasz Cwiklik lukasz.cwiklik]|[uochb.cas.cz" To: CCL Subject: CCL: Help on Molecular Dynamics software Message-Id: <-30928-060218121804-32090-D01zSfnM0pHk4dq0iERBgw ~~ server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1 Date: Sat, 18 Feb 2006 18:17:58 +0100 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [lukasz.cwiklik^uochb.cas.cz] On 2/18/06, HAO JIANG jianghao:_:pitt.edu wrote: > Sent to CCL by: "HAO JIANG" [jianghao..pitt.edu] [...] > I also have a question about making movies from TINKER trajectory files. I know > that ForceFieldExploer of TINKER can display the trajectory, but I don't know how > to save the trajectory animation in other format that is replayable in, say, Microsoft > PowerPoint presentations. Hi, As Lubos Vrbka noticed in this thread, the easiest way to create a movie from TINKER's trajectory file is to use VMD software. You just have to convert trajectory files (*.001, *.002, etc) to a single *.arc file (use "archive" script which is a part of tinkers package). These *.arc files are recognized by VMD, can be visualized as a movie and converted to mpeg format. Best regards, Lukasz -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Sun Feb 19 20:14:00 2006 From: "Eric Scerri scerri * chem.ucla.edu" To: CCL Subject: CCL: eugen schwarz on orbitals Message-Id: <-30929-060218003924-26051-Gm9TXRY9fCMIhXZ//7tUjg%x%server.ccl.net> X-Original-From: Eric Scerri Content-Type: multipart/alternative; boundary=Apple-Mail-3-872680420 Date: Fri, 17 Feb 2006 21:39:13 -0800 Mime-Version: 1.0 (Apple Message framework v746.2) Sent to CCL by: Eric Scerri [scerri:_:chem.ucla.edu] --Apple-Mail-3-872680420 Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed I am wondering what list members think about the article on observation of orbitals in the latest issue of Angewandte Chemie (Int Ed')? If indeed orbitals can be observed in the various senses that Schwarz indicates, how should textbook accounts on the unobservability of orbitals be modified? This is not something that the author addresses. regards, Dr. Eric Scerri Department of Chemistry & Biochemistry, Charles Young Drive, Los Angeles, CA 90095. 310 206 7443 fax: 310 206 2061 UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ Editor of Foundations of Chemistry, http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, 00.html International Society for the Philosophy of Chemistry, http://ispc.sas.upenn.edu/ --Apple-Mail-3-872680420 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1


I am wondering what list members = think about the article on observation of orbitals in the latest issue = of Angewandte Chemie (Int Ed')?

If indeed orbitals can be = observed in the various senses that Schwarz indicates, how should = textbook accounts on the unobservability of orbitals be modified?=A0 = This is not something that the author addresses.=A0=A0

regards,



Dr. Eric = Scerri
Department of Chemistry & = Biochemistry,
Charles Young Drive,
Los = Angeles,
CA 90095.

310 206 7443
fax: = 310 206 2061

UCLA faculty web page:=A0=A0=A0=




= --Apple-Mail-3-872680420-- From owner-chemistry@ccl.net Sun Feb 19 22:49:00 2006 From: "Brian Salter-Duke b_duke/a\octa4.net.au" To: CCL Subject: CCL: eugen schwarz on orbitals Message-Id: <-30930-060219213005-21281-pZU31dnbQER9LD3vfBYgSQ{:}server.ccl.net> X-Original-From: Brian Salter-Duke Content-Disposition: inline Content-Type: text/plain; charset=us-ascii Date: Mon, 20 Feb 2006 13:29:08 +1100 Mime-Version: 1.0 Sent to CCL by: Brian Salter-Duke [b_duke###octa4.net.au] Eric, Could you give us an actual reference? It is not in the latest issue I can access on the web. Regards, Brian. On Sun, Feb 19, 2006 at 08:32:53PM -0500, Eric Scerri scerri * chem.ucla.edu wrote: > Sent to CCL by: Eric Scerri [scerri:_:chem.ucla.edu] > > > --Apple-Mail-3-872680420 > Content-Transfer-Encoding: 7bit > Content-Type: text/plain; > charset=US-ASCII; > delsp=yes; > format=flowed > > > > I am wondering what list members think about the article on > observation of orbitals in the latest issue of Angewandte Chemie (Int > Ed')? > > If indeed orbitals can be observed in the various senses that Schwarz > indicates, how should textbook accounts on the unobservability of > orbitals be modified? This is not something that the author addresses. > > regards, > > > > Dr. Eric Scerri > Department of Chemistry & Biochemistry, > Charles Young Drive, > Los Angeles, > CA 90095. > > 310 206 7443 > fax: 310 206 2061 > > UCLA faculty web page: http://www.chem.ucla.edu/dept/Faculty/scerri/ > > Editor of Foundations of Chemistry, > http://www.springer.com/sgw/cda/frontpage/0,11855,4-40399-70-35545882- > detailsPage%253Djournal%257CmostViewedArticles%257CmostViewedArticles, > 00.html > > International Society for the Philosophy of Chemistry, > http://ispc.sas.upenn.edu/ > > > > > > --Apple-Mail-3-872680420 > Content-Transfer-Encoding: quoted-printable > Content-Type: text/html; > charset=ISO-8859-1 > > -khtml-line-break: after-white-space; ">

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I am wondering what list members = > think about the article on observation of orbitals in the latest issue = > of Angewandte Chemie (Int Ed')?

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If indeed orbitals can be = > observed in the various senses that Schwarz indicates, how should = > textbook accounts on the unobservability of orbitals be modified?=A0 = > This is not something that the author addresses.=A0=A0

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regards,

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class=3D"Apple-style-span" style=3D"border-collapse: separate; = > border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; = > font-size: 16px; font-style: normal; font-variant: normal; font-weight: = > normal; letter-spacing: normal; line-height: normal; text-align: auto; = > -khtml-text-decorations-in-effect: none; text-indent: 0px; = > -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = > white-space: normal; widows: 2; word-spacing: 0px; "> class=3D"Apple-style-span" style=3D"border-collapse: separate; = > border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; = > font-size: 16px; font-style: normal; font-variant: normal; font-weight: = > normal; letter-spacing: normal; line-height: normal; text-align: auto; = > -khtml-text-decorations-in-effect: none; text-indent: 0px; = > -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = > white-space: normal; widows: 2; word-spacing: 0px; "> class=3D"Apple-style-span" style=3D"border-collapse: separate; = > border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; = > font-size: 16px; font-style: normal; font-variant: normal; font-weight: = > normal; letter-spacing: normal; line-height: normal; text-align: auto; = > -khtml-text-decorations-in-effect: none; text-indent: 0px; = > -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = > white-space: normal; widows: 2; word-spacing: 0px; "> class=3D"Apple-style-span" style=3D"border-collapse: separate; = > border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; = > font-size: 16px; font-style: normal; font-variant: normal; font-weight: = > normal; letter-spacing: normal; line-height: normal; text-align: auto; = > -khtml-text-decorations-in-effect: none; text-indent: 0px; = > -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = > white-space: normal; widows: 2; word-spacing: 0px; "> class=3D"Apple-style-span" style=3D"border-collapse: separate; = > border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; = > font-size: 16px; font-style: normal; font-variant: normal; font-weight: = > normal; letter-spacing: normal; line-height: normal; text-align: auto; = > -khtml-text-decorations-in-effect: none; text-indent: 0px; = > -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = > white-space: normal; widows: 2; word-spacing: 0px; "> class=3D"Apple-style-span" style=3D"border-collapse: separate; = > border-spacing: 0px 0px; color: rgb(0, 0, 0); font-family: Helvetica; = > font-size: 16px; font-style: normal; font-variant: normal; font-weight: = > normal; letter-spacing: normal; line-height: normal; text-align: auto; = > -khtml-text-decorations-in-effect: none; text-indent: 0px; = > -apple-text-size-adjust: auto; text-transform: none; orphans: 2; = > white-space: normal; widows: 2; word-spacing: 0px; ">
Dr. Eric = > Scerri
Department of Chemistry & = > Biochemistry,
Charles Young Drive,
Los = > Angeles,
CA 90095.

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310 206 7443
fax: = > 310 206 2061

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UCLA faculty web page:=A0=A0=A0= > class=3D"Apple-style-span" color=3D"#0021E7"> class=3D"Apple-style-span" style=3D"color: rgb(0, 33, 231); = > -khtml-text-decorations-in-effect: underline; "> class=3D"Apple-style-span" style=3D"color: rgb(0, 33, 231); = > -khtml-text-decorations-in-effect: underline; = > ">http://www.chem.ucla.edu/dept/Faculty/scerri/ DIV>

Editor of = > Foundations of Chemistry,

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International Society for = > the Philosophy of Chemistry,
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= > > --Apple-Mail-3-872680420--> > > -- Brian Salter-Duke (Brian Duke) b_duke(0)octa4.net.au Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ.