From owner-chemistry@ccl.net Thu Aug 27 04:25:01 2009 From: "steinbrt]![rci.rutgers.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40088-090827035521-21195-FEyjc+/TggjDV3qDFEtT0Q _ server.ccl.net> X-Original-From: steinbrt---rci.rutgers.edu Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Thu, 27 Aug 2009 03:24:14 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: steinbrt+/-rci.rutgers.edu Dear CCLers, while we are veering far away from computational into philosophical territory here, I would like to add my two cents to this and hope to get some feedback from people with more experience teaching science. > science and encourage young people (e.g., high-school students) to learn > more. Moreover, we want to break the existing attitude that science is > boring and unattractive. Science is fun and doing science is cool - this > is the most important message of the film. While I liked your movie, I dont believe that this is a good impression to convey to new or prospective students. It only sets them up for inevitable disappointment when they find out that doing and learning science is not really fun, but tedious, hard and often boring work (no one who ever debugged parallel code could disagree...) I don't want to depreciate my own profession, because obviously the results of doing research are worth every bit of effort. As an analogy, the Golden Gate Bridge surely is impressive, but I don't think it was fun to build. Wouldn't it be more important to try to make students see the big picture, i.e. that mastering the skills of a scientist, while a huge investment of time and nerves, will 'pay off' in the end? Kind Regards, Dr. Thomas Steinbrecher Institut für physikalische Chemie Albertstr. 23a 79108 Freiburg From owner-chemistry@ccl.net Thu Aug 27 06:41:01 2009 From: "Andreas Bick andreas.bick_+_scienomics.com" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40089-090827062910-29086-/XuwdWNfG2AtSUTC08/R8A:_:server.ccl.net> X-Original-From: Andreas Bick Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1; format=flowed Date: Thu, 27 Aug 2009 11:47:07 +0200 MIME-Version: 1.0 Sent to CCL by: Andreas Bick [andreas.bick!A!scienomics.com] Dear CCLers, while I very much like the idea of the video, i.e. to showcase science in an attractive way to people who might be interested, the main problem in my opinion is that the message is just too much simplified. Students might get a rough awakening if they really take on science for their studies. To use everyday tools and surroundings to explain as done in the video is great, but to be a bit more precise in the message is probably a good way forward. Best regards Andreas > Sent to CCL by: steinbrt+/-rci.rutgers.edu > Dear CCLers, > > while we are veering far away from computational into philosophical > territory here, I would like to add my two cents to this and hope to get > some feedback from people with more experience teaching science. > >> science and encourage young people (e.g., high-school students) to learn >> more. Moreover, we want to break the existing attitude that science is >> boring and unattractive. Science is fun and doing science is cool - this >> is the most important message of the film. > > While I liked your movie, I dont believe that this is a good impression to > convey to new or prospective students. It only sets them up for inevitable > disappointment when they find out that doing and learning science is not > really fun, but tedious, hard and often boring work (no one who ever > debugged parallel code could disagree...) I don't want to depreciate my > own profession, because obviously the results of doing research are worth > every bit of effort. As an analogy, the Golden Gate Bridge surely is > impressive, but I don't think it was fun to build. > > Wouldn't it be more important to try to make students see the big picture, > i.e. that mastering the skills of a scientist, while a huge investment of > time and nerves, will 'pay off' in the end? > > Kind Regards, > > Dr. Thomas Steinbrecher > Institut für physikalische Chemie > Albertstr. 23a > 79108 Freiburg> > > -- Dr. Andreas Bick Scienomics SARL Sales and Marketing phone: +492311385847 mobile: +4916096873623 From owner-chemistry@ccl.net Thu Aug 27 11:24:00 2009 From: "Steve George spgeorge{:}ucsd.edu" To: CCL Subject: CCL: ADF Basis Sets Message-Id: <-40090-090827112042-18306-vlDMlFbDwyHi/Uyw8Djuhg{}server.ccl.net> X-Original-From: "Steve George" Date: Thu, 27 Aug 2009 11:20:38 -0400 Sent to CCL by: "Steve George" [spgeorge++ucsd.edu] Is it possible to specify different basis sets for different atoms in ADF? For instance, how do you code a job where carbon atoms use TZ2P and some metal atom used QZ4P? THanks in advance! Steve George spgeorge:+:ucsd.edu From owner-chemistry@ccl.net Thu Aug 27 12:53:01 2009 From: "Reinaldo Pis Diez reinaldo.pisdiez\a/gmail.com" To: CCL Subject: CCL: ADF Basis Sets Message-Id: <-40091-090827124331-19281-DkToLcB/I+VVYZFo9dqjsA-$-server.ccl.net> X-Original-From: Reinaldo Pis Diez Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 Aug 2009 13:36:23 -0300 MIME-Version: 1.0 Sent to CCL by: Reinaldo Pis Diez [reinaldo.pisdiez*gmail.com] Yes, it is possible. Use the create keyword to generate the fragments with the basis you want and then use the fragments keyword in your input to tell ADF to attach the files. Look for those keywords in the manual. Regards, Reinaldo Steve George spgeorge{:}ucsd.edu escribió: > Sent to CCL by: "Steve George" [spgeorge++ucsd.edu] > Is it possible to specify different basis sets for > different atoms in ADF? For instance, how do you code a job where carbon atoms > use TZ2P and some metal atom used QZ4P? > > THanks in advance! > > Steve George > spgeorge(0)ucsd.edu> > > From owner-chemistry@ccl.net Thu Aug 27 13:28:00 2009 From: "Mihaly Mezei Mihaly.Mezei]*[mssm.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40092-090827125715-21940-0Z7+jbSqWtt9gqWMQqMaaA-.-server.ccl.net> X-Original-From: Mihaly Mezei Content-disposition: inline Content-language: en Content-transfer-encoding: 7BIT Content-type: text/plain; charset=us-ascii Date: Thu, 27 Aug 2009 12:57:02 -0400 MIME-version: 1.0 Sent to CCL by: Mihaly Mezei [Mihaly.Mezei]_[mssm.edu] > While I liked your movie, I dont believe that this is a good impression to > convey to new or prospective students. It only sets them up for > inevitable disappointment when they find out that doing and learning > science is not really fun, but tedious, hard and often boring work (no one who ever > debugged parallel code could disagree...) I don't want to depreciate my > own profession, because obviously the results of doing research are > worth every bit of effort. As an analogy, the Golden Gate Bridge > surely is impressive, but I don't think it was fun to build. I agree with Dr. Steinbrecher. Also, I would like to point out that the "fun" we are having when doing science (and we do) is very different from the "fun" of, say, attending a rock concert. To me, the "fun" is when after a tedious derivation, the pesky higher order terms cancel and I end up with a closed form result. Or, when after weeks of coding, debugging and testing, an idea I had turns out to be correct. Or, after half an hour of head scratching, I manage to solve a Sudoku labeled 'hard'. Maybe the closest analogy would be a strenuous hike to a spot with spectacular view. I think that this is the idea of fun that we have to convey to the future generation. Mihaly Mezei Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU Voice: (212) 659-5475 Fax: (212) 849-2456 WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632 WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei WWW (Department): http://atlas.physbio.mssm.edu From owner-chemistry@ccl.net Thu Aug 27 14:05:00 2009 From: "Nuno A. G. Bandeira nuno.bandeira{}ist.utl.pt" To: CCL Subject: CCL: ADF Basis Sets Message-Id: <-40093-090827130405-24976-bvNxekP5mXUoFpr+u4/7vQ|-|server.ccl.net> X-Original-From: "Nuno A. G. Bandeira" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 27 Aug 2009 18:28:50 +0200 MIME-Version: 1.0 Sent to CCL by: "Nuno A. G. Bandeira" [nuno.bandeira__ist.utl.pt] Steve George spgeorge{:}ucsd.edu wrote: > Sent to CCL by: "Steve George" [spgeorge++ucsd.edu] > Is it possible to specify different basis sets for > different atoms in ADF? For instance, how do you code a job where carbon atoms > use TZ2P and some metal atom used QZ4P? Like so: BASIS C TZ2P/C.1s O TZ2P/O.1s ... END -- Nuno A. G. Bandeira, AMRSC Laboratoire de Chimie LR6 Ecole Normale Superieure de Lyon 46, Allee d'Italie 69364 Lyon Cedex 07 - France http://cqb.fc.ul.pt/intheochem/nuno.html -- From owner-chemistry@ccl.net Thu Aug 27 15:27:00 2009 From: "N. Sukumar nagams!=!rpi.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40094-090827145338-5880-adt7VlczUyYyJAHbkK4vKw]-[server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 27 Aug 2009 13:42:47 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams-,-rpi.edu] I too feel that the video is oversimplified to the point of confusing the concepts involved and would have liked to see more thought go into developing the analogies employed. But I'd like to address here Dr. Steinbrecher's comment that it "sets them [students] up for inevitable disappointment when they find out that doing and learning science is not really fun, but tedious, hard and often boring work." I think many of us get trapped into this kind thinking, assuming that we teach science for science's sake. Certainly at the high school and middle school level - and even at the undergraduate level - this is not and should not be true. Teaching science as if it is intended only for - or primarily for - scientists, leads to a general population that is disconnected from science and has no appreciation for science. Given the nature of the problems facing the world today (and seeing the sorry level of political discourse around us), we can ill afford to have a scientifically illiterate general public. "Mastering the skills of a scientist" can come later, as and when needed: the vast majority of those we should be teaching science to will never become scientists, but their level and depth of scientific understanding will be crucial to our future. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ ==============Original message text=============== On Thu, 27 Aug 2009 5:47:07 EDT "Andreas Bick andreas.bick_+_scienomics.com" wrote: Sent to CCL by: Andreas Bick [andreas.bick!A!scienomics.com] Dear CCLers, while I very much like the idea of the video, i.e. to showcase science in an attractive way to people who might be interested, the main problem in my opinion is that the message is just too much simplified. Students might get a rough awakening if they really take on science for their studies. To use everyday tools and surroundings to explain as done in the video is great, but to be a bit more precise in the message is probably a good way forward. Best regards Andreas > Sent to CCL by: steinbrt+/-rci.rutgers.edu > Dear CCLers, > > while we are veering far away from computational into philosophical > territory here, I would like to add my two cents to this and hope to get > some feedback from people with more experience teaching science. > >> science and encourage young people (e.g., high-school students) to learn >> more. Moreover, we want to break the existing attitude that science is >> boring and unattractive. Science is fun and doing science is cool - this >> is the most important message of the film. > > While I liked your movie, I dont believe that this is a good impression to > convey to new or prospective students. It only sets them up for inevitable > disappointment when they find out that doing and learning science is not > really fun, but tedious, hard and often boring work (no one who ever > debugged parallel code could disagree...) I don't want to depreciate my > own profession, because obviously the results of doing research are worth > every bit of effort. As an analogy, the Golden Gate Bridge surely is > impressive, but I don't think it was fun to build. > > Wouldn't it be more important to try to make students see the big picture, > i.e. that mastering the skills of a scientist, while a huge investment of > time and nerves, will 'pay off' in the end? > > Kind Regards, > > Dr. Thomas Steinbrecher > Institut für physikalische Chemie > Albertstr. 23a > 79108 Freiburg> > > -- Dr. Andreas Bick Scienomics SARL Sales and Marketing phone: +492311385847 mobile: +4916096873623http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt===========End of original message text=========== From owner-chemistry@ccl.net Thu Aug 27 16:02:01 2009 From: "Johannes Johansson johjo76++gmail.com" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40095-090827153355-16686-aaDUj9UZEfjEkzLElTdzkQ^-^server.ccl.net> X-Original-From: Johannes Johansson Content-Type: multipart/alternative; boundary=000e0cd356c833ee7d047224343a Date: Thu, 27 Aug 2009 21:02:07 +0200 MIME-Version: 1.0 Sent to CCL by: Johannes Johansson [johjo76+/-gmail.com] --000e0cd356c833ee7d047224343a Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: quoted-printable To those who are following the (more or less useful) discussion of the YouTube clip on the interaction of matter and light. There is a thesis in Physics Pedagogics, published in 2007 at Uppsala University, Sweden. It deals with WHAT students of chemistry and physics find most difficult in QM (at different levels) and it also tries to track the reasons for this difficulties and misunderstandings. ONE of the conclusions is that the teaching of simplified models such as the pictorial Bohr atom causes difficulties also for students at higher levels. This is NOT a personal statement from me, just some information for those who are interested in this issue, so please do not give me any replies. If you are interested, please see: http://uu.diva-portal.org/smash/record.jsf?searchId=3D1&pid=3Ddiva2:116635 or http://johanfalk.net/sites/default/files/Falk_2007_licentiate%20thesis.pdf Kind regards/Johannes 2009/8/27 Mihaly Mezei Mihaly.Mezei]*[mssm.edu > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei]_[mssm.edu] > > While I liked your movie, I dont believe that this is a good impressio= n > to > > convey to new or prospective students. It only sets them up for > > inevitable disappointment when they find out that doing and learning > > science is not really fun, but tedious, hard and often boring work (no > one who ever > > debugged parallel code could disagree...) I don't want to depreciate my > > own profession, because obviously the results of doing research are > > worth every bit of effort. As an analogy, the Golden Gate Bridge > > surely is impressive, but I don't think it was fun to build. > > I agree with Dr. Steinbrecher. > > Also, I would like to point out that the "fun" we are having when doing > science (and we do) is very different from the "fun" of, say, attending a > rock concert. To me, the "fun" is when after a tedious derivation, the pe= sky > higher order terms cancel and I end up with a closed form result. Or, whe= n > after weeks of coding, debugging and testing, an idea I had turns out to = be > correct. Or, after half an hour of head scratching, I manage to solve a > Sudoku labeled 'hard'. Maybe the closest analogy would be a strenuous hi= ke > to a spot with spectacular view. I think that this is the idea of fun tha= t > we have to convey to the future generation. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of > Medicine, NYU > Voice: (212) 659-5475 Fax: (212) 849-2456 > WWW (MSSM home): > http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=3D000007250000= 1497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > > > > -=3D This is automatically added to each message by the mailing script = =3D-> > > --=20 Adam Johannes Johansson Ph.D., M.Sc. Institut f=C3=BCr Organische Chemie RWTH Aachen University Landoltweg 1 52056 Aachen Germany Cell phone:0708178487 E-mail:johjo76_-_gmail.com Research web page:www.physto.se/~johjo --000e0cd356c833ee7d047224343a Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable To those who are following the (more or less useful) discussion of the YouT= ube clip on the interaction of matter and light. There is a thesis in Physi= cs Pedagogics, published in 2007 at Uppsala University, Sweden. It deals wi= th WHAT=C2=A0<= /span>students of chemistry and physics find most difficult in QM (at diffe= rent levels) and it also tries to track the reasons for this difficulties a= nd misunderstandings. ONE of the conclusions is that the teaching of simpli= fied models such as the pictorial Bohr atom causes difficulties also for st= udents at higher levels. This is NOT a personal statement from me, just som= e information for those who are interested in this issue, so please do not = give me any replies. If you are interested, please see:


or

Kind regards/Johannes




2009/8/27 Mihaly Mezei Mihaly.Mezei]*[mssm.edu= <owner= -chemistry_-_ccl.net>

Sent to CCL by: Mihaly Mezei [Mihaly.Mezei]_[mssm.edu]
> While I liked your movie, I dont believe that this is a good =C2=A0imp= ression to
> convey to new or prospective students. It only sets them up for
> inevitable disappointment when they find out that doing and learning > science is not really fun, but tedious, hard and often boring work (no= one who ever
> debugged parallel code could disagree...) I don't want to deprecia= te my
> own profession, because obviously the results of doing research are > worth every bit of effort. As an analogy, the Golden Gate Bridge
> surely is impressive, but I don't think it was fun to build.

I agree with Dr. Steinbrecher.

Also, I would like to point out that the "fun" we are having when= doing science (and we do) is very different from the "fun" of, s= ay, attending a rock concert. To me, the "fun" is when after a te= dious derivation, the pesky higher order terms cancel and I end up with a c= losed form result. Or, when after weeks of coding, debugging and testing, a= n idea I had turns out to be correct. Or, after half an hour of head scratc= hing, I manage to solve a Sudoku labeled 'hard'. =C2=A0Maybe the cl= osest analogy would be a strenuous hike to a spot with spectacular view. I = think that this is the idea of fun that we have to convey to the future gen= eration.

Mihaly Mezei

Department of Structural and Chemical Biology, Mount Sinai School of Medici= ne, NYU
Voice: =C2=A0(212) 659-5475 =C2=A0 Fax: (212) 849-2456
WWW (MSSM home): http://www.mountsin= ai.org/Find%20A%20Faculty/profile.do?id=3D0000072500001497192632
WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei
WWW (Department): http://atlas.physbio.mssm.edu



-=3D This is automatically added to each message by the mailing script =3D-=
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--
Adam Johannes Johansson=
Ph.D., M.Sc.
Institut f=C3=BCr Organische Chemie
RWTH Aachen Univ= ersity
Landoltweg 1
52056 Aachen
Germany
Cell phone:0708178487<= br> E-mail:johjo76_-_gmail.com<= br>Research web page:www.physto.se/= ~johjo

--000e0cd356c833ee7d047224343a-- From owner-chemistry@ccl.net Thu Aug 27 16:41:01 2009 From: "Mark Zottola mzottola[a]gmail.com" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40096-090827161043-6790-yOZkG3mV2ruB3cwK00uDJA|*|server.ccl.net> X-Original-From: Mark Zottola Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 27 Aug 2009 16:10:22 -0400 MIME-Version: 1.0 Sent to CCL by: Mark Zottola [mzottola!A!gmail.com] Normally I just read posts like this and let life move on.=A0 But I feel compelled to put in my two cents. First, as a tool to get high school students interested in science, I think it is a GREAT idea!=A0 I grew up learning about valence shell electrons in circular orbits around a nucleus.=A0 Was that WRONG? Should I have been given a quantum mechanics text at age 5 and told to learn it or forget about chemistry?=A0 This is a WONDERFUL idea to bring scientific concepts to students who are barraged by (at least the American) media that "Science is Really Hard!"=A0 As a result great scientific minds get seduced by the siren's call of money.=A0 Instead these lost minds go into Business and Finance.=A0 If recent events are not enough to convince people that poorly focused minds can bring great destruction, there is no hope for you. Secondly, as a University professor who regularly mentored high school students, there is nothing that kindles excitement more in young minds than the hope of understanding.=A0 I had students working on projects involving special relativity, kinetic behaviour of noble gases and even quantum mechanics.=A0 These students hungrily tore into their projects because they had an understanding.=A0 I did not use You-Tube or other media sources.=A0 I did it the old-fashioned way.=A0=A0Many=A0high school students that experience true=A0mentorship have an unbounded enthusiasm that translates into learning science in a way deeper and more fully than any classroom. Finally, with all due respect - Science is FUN!=A0 While it is hard work, while there is much angst, it is still fun.=A0 We uncover the secrets of life, the mysteries of the universe!=A0 We have tools to help us see beyond the horizons.=A0 We share our knowledge in the hope of making a better world for all of us.=A0 We are Lewis and Clark, we are Captain Cook and Magellan, we are Sir Edmund Hillary, we are all that and something more!=A0 How can this NOT be fun?=A0 Ever play baseball and been hit by a pitch, ever get beaten by a midfielder with fresher legs in the 80th minute,=A0ever get an elbow when going up for a rebound? Not fun, not at all, yet it is part of the joy of sports that people endure all this!=A0 Yeah we struggle with experiments,=A0derivations and confusing results, but we do it because it is, in our hearts, fun! If science is not fun, please do find your life's work and enjoy that. Life is too short. On Thu, Aug 27, 2009 at 12:57 PM, Mihaly Mezei Mihaly.Mezei]*[mssm.edu wrote: > > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei]_[mssm.edu] > > While I liked your movie, I dont believe that this is a good =A0impress= ion to > > convey to new or prospective students. It only sets them up for > > inevitable disappointment when they find out that doing and learning > > science is not really fun, but tedious, hard and often boring work (no = one who ever > > debugged parallel code could disagree...) I don't want to depreciate my > > own profession, because obviously the results of doing research are > > worth every bit of effort. As an analogy, the Golden Gate Bridge > > surely is impressive, but I don't think it was fun to build. > > I agree with Dr. Steinbrecher. > > Also, I would like to point out that the "fun" we are having when doing s= cience (and we do) is very different from the "fun" of, say, attending a ro= ck concert. To me, the "fun" is when after a tedious derivation, the pesky = higher order terms cancel and I end up with a closed form result. Or, when = after weeks of coding, debugging and testing, an idea I had turns out to be= correct. Or, after half an hour of head scratching, I manage to solve a Su= doku labeled 'hard'. =A0Maybe the closest analogy would be a strenuous hike= to a spot with spectacular view. I think that this is the idea of fun that= we have to convey to the future generation. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of Medi= cine, NYU > Voice: =A0(212) 659-5475 =A0 Fax: (212) 849-2456 > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?= id=3D0000072500001497192632 > WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei > WWW (Department): http://atlas.physbio.mssm.edu > > > > -=3D This is automatically added to each message by the mailing script = =3D-> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/cgi-bin/ccl/send_ccl_message> =A0 =A0 =A0http://www.ccl.net/chemistry/sub_unsub.shtml> =A0 =A0 =A0http://www.ccl.net/spammers.txt> > From owner-chemistry@ccl.net Thu Aug 27 17:12:00 2009 From: "Marcel Swart marcel.swart.\a/.icrea.es" To: CCL Subject: CCL: ADF Basis Sets Message-Id: <-40097-090827141434-10308-dSTmc4k7q7/tZkHuJp78Ew\a/server.ccl.net> X-Original-From: Marcel Swart Content-Type: multipart/alternative; boundary=Apple-Mail-32-352304214 Date: Thu, 27 Aug 2009 18:18:47 +0200 Mime-Version: 1.0 (Apple Message framework v753.1) Sent to CCL by: Marcel Swart [marcel.swart=icrea.es] --Apple-Mail-32-352304214 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=ISO-8859-1; delsp=yes; format=flowed Yes, very easily: BASIS C $ADFRESOURCES/TZ2P/C.1s Fe $ADFRESOURCES/QZ4P/Fe.2p END On Aug 27, 2009, at 5:20 PM, Steve George spgeorge{:}ucsd.edu wrote: > Is it possible to specify different basis sets for > different atoms in ADF? For instance, how do you code a job where =20 > carbon atoms > use TZ2P and some metal atom used QZ4P? > > THanks in advance! > > Steve George > spgeorge(0)ucsd.edu =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D dr. Marcel Swart ICREA researcher at Institut de Qu=EDmica Computacional Universitat de Girona Parc Cient=EDfic i Tecnol=F2gic Edifici Jaume Casademont (despatx A-27) Pic de Peguera 15 17003 Girona Catalunya (Spain) tel +34-972-183240 fax +34-972-183241 e-mail marcel.swart---icrea.es marcel.swart---udg.edu web http://www.icrea.cat/Web/ScientificForm.aspx?key=3D372 http://iqc.udg.edu/~marcel =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D --Apple-Mail-32-352304214 Content-Transfer-Encoding: quoted-printable Content-Type: text/html; charset=ISO-8859-1

Yes, very easily:

BASIS
  C   = $ADFRESOURCES/TZ2P/C.1s
  Fe =  $ADFRESOURCES/QZ4P/Fe.2p
END

On Aug 27, 2009, at = 5:20 PM, Steve George spgeorge{:}ucsd.edu wrote:

Is it possible to specify = different basis sets for
different = atoms in ADF? For instance, how do you code a job where carbon = atoms
use TZ2P and some metal atom = used QZ4P?

THanks in advance!

Steve = George
spgeorge(0)ucsd.edu
=

dr. Marcel = Swart

ICREA = researcher at
Institut de Qu=EDmica = Computacional
Universitat de = Girona

Parc Cient=EDfic i = Tecnol=F2gic
Edifici Jaume Casademont (despatx = A-27)
17003 Girona
Catalunya = (Spain)

tel
marcel.swart---udg.edu



=

= --Apple-Mail-32-352304214-- From owner-chemistry@ccl.net Thu Aug 27 17:50:00 2009 From: "Basma Ghazal basmaghazal]~[ymail.com" To: CCL Subject: CCL: Steps of docking Message-Id: <-40098-090827164354-32363-rwbWIatBll1nH9WbQnS8bA#%#server.ccl.net> X-Original-From: Basma Ghazal Content-Type: multipart/alternative; boundary="0-723227215-1251402221=:98831" Date: Thu, 27 Aug 2009 12:43:41 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Basma Ghazal [basmaghazal|,|ymail.com] --0-723227215-1251402221=:98831 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Dear All: I am anewly user for docking I need some one who has experence on this fiel= d to tell him If Iam true or not and to=A0see this step with me =A0: (1) dowenload the protien from the pdb=20 (2) preparing it : removing water and adding hydrogen=20 and why we remove the polar hydrogen (3)docking used arguslab and/or autodock ((4) and what after that Thanks=0A=0A=0A --0-723227215-1251402221=:98831 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Dear All:<= /STRONG>
I am anewly user for docking I need some one wh= o has experence on this field to tell him If Iam true or not and to se= e this step with me  :
(1) dowenload the protien from the pdb
(2) preparing it : removing water and adding hydrogen
and w= hy we remove the polar hydrogen
(3)docking used arguslab and/or autodock=
((4)<= /FONT> and what after that
Thanks
<= br>=0A=0A --0-723227215-1251402221=:98831-- From owner-chemistry@ccl.net Thu Aug 27 22:12:00 2009 From: "Morad El-Hendawy m80elhendawy * yahoo.com" To: CCL Subject: CCL: Steps of docking Message-Id: <-40099-090827185356-30013-4GjuFFEF5Zq4C2lBM6WZEg#%#server.ccl.net> X-Original-From: Morad El-Hendawy Content-Type: multipart/alternative; boundary="0-1566391290-1251413616=:57633" Date: Thu, 27 Aug 2009 15:53:36 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: Morad El-Hendawy [m80elhendawy(a)yahoo.com] --0-1566391290-1251413616=:57633 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable Hi, Here you may find your target: http://www.arguslab.com/tutorials.htm My regards, ***************************************************************************= ***********************Morad M. El-Hendawy*********************************= *****************************************************************=A0If you = want a happy life, do four things:=A01- Contemplate and be thankful, 2- The past is gone forever, 3- Today all that you have, 4- Leave the future alone untill it come.=A0*******************************= ***************************************************************************= ********* =A0 --- On Thu, 8/27/09, Basma Ghazal basmaghazal]~[ymail.com wrote: > From: Basma Ghazal basmaghazal]~[ymail.com Subject: CCL: Steps of docking To: "El-Hendawy, Morad Metwally " Date: Thursday, August 27, 2009, 10:43 PM Dear All:=0AI am anewly user for docking I need some one who has experence = on this field to tell him If Iam true or not and to=A0see this step with me= =A0:=0A(1) dowenload the protien from the pdb =0A(2) preparing it : removi= ng water and adding hydrogen =0Aand why we remove the polar hydrogen=0A(3)d= ocking used arguslab and/or autodock=0A((4) and what after that=0AThanks =0A=0A =0A=0A=0A --0-1566391290-1251413616=:57633 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: quoted-printable
Hi,
Here you may find your target:
http= ://www.arguslab.com/tutorials.htm
My regards,
*********************************= *****************************************************************
Mo= rad M. El-Hendawy
********************************************************************= ******************************
 If you want a happy life, do four things:
 
1- Contemplate and be thankful,
2- The past is gone forever,
3-= Today all that you have,
4- Leave the future alone untill it come. 
********************************************************= ***********************************************************=

 


--- On Thu, 8/27/09, Basma Ghazal basmaghaza= l]~[ymail.com <owner-chemistry~!~ccl.net> wrote:

From: Basma Ghazal basmaghazal]~[ymail.com <owner-c= hemistry~!~ccl.net>
Subject: CCL: Steps of docking
To: "El-Hendawy, = Morad Metwally " <m80elhendawy~!~yahoo.com>
Date: Thursday, = August 27, 2009, 10:43 PM

Dear All:
=0A
I am anew= ly user for docking I need some one who has experence on this field to tell= him If Iam true or not and to see this step with me  :
=0A
(1) dowenload the protien from the pdb =
=0A
(2) preparing it : removing water and addin= g hydrogen
=0A
and why we remove the polar hydr= ogen
=0A
(3)dockin= g used arguslab and/or autodock
=0A
((4) = and what after that
=0A
T= hanks

=0A=0A
=

=0A=0A --0-1566391290-1251413616=:57633-- From owner-chemistry@ccl.net Thu Aug 27 22:47:01 2009 From: "N. Sukumar nagams[a]rpi.edu" To: CCL Subject: CCL: And now something completely different! Message-Id: <-40100-090827195246-5900-qamIBRMC0L+rcbU7AWWFrQ+*+server.ccl.net> X-Original-From: "N. Sukumar" Content-Disposition: inline Content-Transfer-Encoding: binary Content-Type: text/plain Date: Thu, 27 Aug 2009 19:52:31 -0400 MIME-Version: 1.0 Sent to CCL by: "N. Sukumar" [nagams . rpi.edu] Hear-hear! Let us teach the FUN in science and scientific concepts to school children and leave the grantsmanship courses to graduate school. If that results in some attrition of less motivated students during graduate school, I think we can live with that. Science is more than just a profession. Even those students who turn away from science will be better off for their exposure to the scientific method and scientific principles; society will benefit as a result. Dr. N. Sukumar Rensselaer Exploratory Center for Cheminformatics Research http://reccr.chem.rpi.edu/ ==============Original message text=============== On Thu, 27 Aug 2009 16:10:22 EDT "Mark Zottola mzottola[a]gmail.com" wrote: Sent to CCL by: Mark Zottola [mzottola!A!gmail.com] Normally I just read posts like this and let life move on.� But I feel compelled to put in my two cents. First, as a tool to get high school students interested in science, I think it is a GREAT idea!� I grew up learning about valence shell electrons in circular orbits around a nucleus.� Was that WRONG? Should I have been given a quantum mechanics text at age 5 and told to learn it or forget about chemistry?� This is a WONDERFUL idea to bring scientific concepts to students who are barraged by (at least the American) media that "Science is Really Hard!"� As a result great scientific minds get seduced by the siren's call of money.� Instead these lost minds go into Business and Finance.� If recent events are not enough to convince people that poorly focused minds can bring great destruction, there is no hope for you. Secondly, as a University professor who regularly mentored high school students, there is nothing that kindles excitement more in young minds than the hope of understanding.� I had students working on projects involving special relativity, kinetic behaviour of noble gases and even quantum mechanics.� These students hungrily tore into their projects because they had an understanding.� I did not use You-Tube or other media sources.� I did it the old-fashioned way.��Many�high school students that experience true�mentorship have an unbounded enthusiasm that translates into learning science in a way deeper and more fully than any classroom. Finally, with all due respect - Science is FUN!� While it is hard work, while there is much angst, it is still fun.� We uncover the secrets of life, the mysteries of the universe!� We have tools to help us see beyond the horizons.� We share our knowledge in the hope of making a better world for all of us.� We are Lewis and Clark, we are Captain Cook and Magellan, we are Sir Edmund Hillary, we are all that and something more!� How can this NOT be fun?� Ever play baseball and been hit by a pitch, ever get beaten by a midfielder with fresher legs in the 80th minute,�ever get an elbow when going up for a rebound? Not fun, not at all, yet it is part of the joy of sports that people endure all this!� Yeah we struggle with experiments,�derivations and confusing results, but we do it because it is, in our hearts, fun! If science is not fun, please do find your life's work and enjoy that. Life is too short. On Thu, Aug 27, 2009 at 12:57 PM, Mihaly Mezei Mihaly.Mezei]*[mssm.edu wrote: > > > Sent to CCL by: Mihaly Mezei [Mihaly.Mezei]_[mssm.edu] > > While I liked your movie, I dont believe that this is a good �impression to > > convey to new or prospective students. It only sets them up for > > inevitable disappointment when they find out that doing and learning > > science is not really fun, but tedious, hard and often boring work (no one who ever > > debugged parallel code could disagree...) I don't want to depreciate my > > own profession, because obviously the results of doing research are > > worth every bit of effort. As an analogy, the Golden Gate Bridge > > surely is impressive, but I don't think it was fun to build. > > I agree with Dr. Steinbrecher. > > Also, I would like to point out that the "fun" we are having when doing science (and we do) is very different from the "fun" of, say, attending a rock concert. To me, the "fun" is when after a tedious derivation, the pesky higher order terms cancel and I end up with a closed form result. Or, when after weeks of coding, debugging and testing, an idea I had turns out to be correct. Or, after half an hour of head scratching, I manage to solve a Sudoku labeled 'hard'. �Maybe the closest analogy would be a strenuous hike to a spot with spectacular view. I think that this is the idea of fun that we have to convey to the future generation. > > Mihaly Mezei > > Department of Structural and Chemical Biology, Mount Sinai School of Medicine, NYU > Voice: �(212) 659-5475 � Fax: (212) 849-2456 > WWW (MSSM home): http://www.mountsinai.org/Find%20A%20Faculty/profile.do?id=0000072500001497192632> WWW (Lab home - software, publications): http://inka.mssm.edu/~mezei> WWW (Department): http://atlas.physbio.mssm.edu> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message> � � �http://www.ccl.net/cgi-bin/ccl/send_ccl_message> � � �http://www.ccl.net/chemistry/sub_unsub.shtml> � � �http://www.ccl.net/spammers.txthttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlJob: http://www.ccl.net/jobshttp://www.ccl.net/spammers.txt===========End of original message text===========