From owner-chemistry@ccl.net Mon Jul 17 00:52:03 2006 From: "Jianhui lan lanjh03|a|sohu.com" To: CCL Subject: CCL: I need a template for NEB calculation Message-Id: <-32152-060716090657-18957-v3oAgysm9gcjYmprNgE/qA#server.ccl.net> X-Original-From: "Jianhui lan" Date: Sun, 16 Jul 2006 08:48:35 -0400 Sent to CCL by: "Jianhui lan" [lanjh03%x%sohu.com] I want to investigate the surface diffusion phenomenon with vasp software. But now I am confronted with the question that which software can I use to construct the slab. Can anyone give me some advice? From owner-chemistry@ccl.net Mon Jul 17 03:45:01 2006 From: "Wai-To Chan chan%curl.gkcl.yorku.ca" To: CCL Subject: CCL:G: Can we find the transition state of SN1 reaction by using Message-Id: <-32153-060717033911-10775-x9kPYGus37BsbmuE8jh3pw[*]server.ccl.net> X-Original-From: Wai-To Chan Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Date: Mon, 17 Jul 2006 03:39:19 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Wai-To Chan [chan^_^curl.gkcl.yorku.ca] <<<<<<<<<<<<<<<<<<<<<<, Dear all, Recently I have failed to find the transition state of the first step of solvolyses of alkyl halide RX,for example tert-Butylchloride in methanol solvent by using Gaussian03. RX->R+ + X- Following the lengths of C-Cl increasing,the potential energy rises all along,which is the same with the case of in methanol solvent by using PCM model. ......................................... >>>>>>>>>>>>>>>>>>>>>>.. Can't comment on the role of solvent effect. As far as calculating the potential profile for the extension of the R---X bond in the gas phase goes bear these two things in mind: In addition to the R+ + X- channel dissociation of RX can also give you two doublet radicals R and X. The RHF method is not expected to give you a qualitatively correct potential profile for bond stretching beyond the point where wavefunction instability sets in. Assuming a transition state exists near the dissociation asymptote of R+/X- RHF-based correlated method or RDFT would also fail like RHF. Wai-To Chan From owner-chemistry@ccl.net Mon Jul 17 04:42:00 2006 From: "Eduardo Lemos de Sa edulsa^^^quimica.ufpr.br" To: CCL Subject: CCL: force-fields Message-Id: <-32154-060717043700-20024-ATJSSuYdIiGPX/hqaKaZSw~~server.ccl.net> X-Original-From: "Eduardo Lemos de Sa" Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 17 Jul 2006 04:33:26 -0300 (BRT) MIME-Version: 1.0 Sent to CCL by: "Eduardo Lemos de Sa" [edulsa**quimica.ufpr.br] Sirs and Ladies A friend of mine ask the question bellow: "Is there a non-commercially available source-code that accepts a user defined force-field and has a built in geometry optimizer that allows to superimpose valence constraints such as fixed torsion angles etc?" I will summarize to CCL the suggsetions Thank you in advance for your attention Eduardo -- Eduardo Lemos de Sa edulsa**quimica.ufpr.br Professor Adj. IV - Departamento de Quimica Universidade Federal do Parana C. P. 19081 81531-990 Curitiba/PR - Brazil Fone (41) 3361 3300 From owner-chemistry@ccl.net Mon Jul 17 05:16:01 2006 From: "Dr Noko Phala nokophala*aim.com" To: CCL Subject: CCL: magnetic field Message-Id: <-32155-060716133944-4392-0v0l2ezzWJBysiMbb23pPQ]![server.ccl.net> X-Original-From: "Dr Noko Phala" Content-Language: i-default Content-Type: multipart/alternative; boundary="EPOC32--HL53PRcQpNRVBhb3Vt8cttR,StVGTw3pc4p49cy6wrGTZV5" Date: Sun, 16 Jul 2006 19:02:49 +0200 MIME-Version: 1.0 Sent to CCL by: "Dr Noko Phala" [nokophala_+_aim.com] --EPOC32--HL53PRcQpNRVBhb3Vt8cttR,StVGTw3pc4p49cy6wrGTZV5 Content-Type: text/plain; charset=UTF-8 Content-Disposition: inline Content-Transfer-Encoding: quoted-printable Hi, Does anyone have a scheme for calculating electronic structure (orbital ener= gies,total energies,orbital symmetries,etc) of a material in the presence of= a magnetic field,in the same way as that similar calculations in the prese= nce of an electric field can routely be performed? Thanks, Noko P.=20 --EPOC32--HL53PRcQpNRVBhb3Vt8cttR,StVGTw3pc4p49cy6wrGTZV5 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: base64 PCFET0NUWVBFIEhUTUwgUFVCTElDICItLy9XM0MvL0RURCBIVE1MIDMuMiBGaW5hbC8vRU4i Pgo8SFRNTD4gCjxIRUFEPiAKPFRJVExFPkNvbnZlcnRlZCBmcm9tIFJpY2ggVGV4dDwvVElU TEU+CjxNRVRBIEhUVFAtRVFVSVY9IkNvbnRlbnQtVHlwZSIgQ09OVEVOVD0idGV4dC9odG1s OyBjaGFyc2V0PVVURi04Ij48TUVUQSBOQU1FPSJnZW5lcmF0b3IiIENPTlRFTlQ9InJ0Mmh0 bWwgY29udmVydGVyIj4KPC9IRUFEPiAKPEJPRFkgQkdDT0xPUj0iI2ZmZmZmZiIgVEVYVD0i IzAwMDAwMCI+CjxESVYgQUxJR049TEVGVD5IaSw8L0RJVj4gCjxESVYgQUxJR049TEVGVD5E b2VzIGFueW9uZSBoYXZlIGEgc2NoZW1lIGZvciBjYWxjdWxhdGluZyBlbGVjdHJvbmljIHN0 cnVjdHVyZSAob3JiaXRhbCBlbmVyZ2llcyx0b3RhbCBlbmVyZ2llcyxvcmJpdGFsIHN5bW1l dHJpZXMsZXRjKSBvZiBhIG1hdGVyaWFsIGluIHRoZSBwcmVzZW5jZSBvZiBhIG1hZ25ldGlj IGZpZWxkLGluIHRoZSBzYW1lIHdheSBhcyB0aGF0IHNpbWlsYXIgIGNhbGN1bGF0aW9ucyBp biB0aGUgcHJlc2VuY2Ugb2YgYW4gZWxlY3RyaWMgZmllbGQgY2FuIHJvdXRlbHkgYmUgcGVy Zm9ybWVkPzwvRElWPiAKPERJViBBTElHTj1MRUZUPiZuYnNwOzwvRElWPjxESVYgQUxJR049 TEVGVD5UaGFua3MsPC9ESVY+IAo8RElWIEFMSUdOPUxFRlQ+Tm9rbyBQLiA8L0RJVj4gCjxE SVYgQUxJR049TEVGVD48L0RJVj4gCjwvQk9EWT4KPC9IVE1MPiAK --EPOC32--HL53PRcQpNRVBhb3Vt8cttR,StVGTw3pc4p49cy6wrGTZV5-- From owner-chemistry@ccl.net Mon Jul 17 09:39:01 2006 From: "Shobe, David dshobe---sud-chemieinc.com" To: CCL Subject: CCL:G: Can we find the transition state of SN1 reaction by using Message-Id: <-32156-060717091451-26586-hG58VXazQpuDwbExVCaUvw||server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 17 Jul 2006 15:14:10 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe!=!sud-chemieinc.com] I'm going to have to say "me too" on this one. Although it superficially resembles the case I discussed earlier, in which I argued that there might not be a TS, your situation is different. For the R+ and X- to react in solution, the solvent molecules separating them have to be moved out of the way. This will cost energy, so there should be a transition state in solution. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry++ccl.net [mailto:owner-chemistry++ccl.net] Sent: Sunday, July 16, 2006 12:49 PM To: Shobe, David Subject: CCL:G: Can we find the transition state of SN1 reaction by using Sent to CCL by: Steve Bowlus [chezbowlus!A!goldrush.com] It would not surprise me that this type of reaction must be modeled with explicit solvent. Stabilization of the products relative to the TS is attained by solvation of the separated ions, i.e. the physical "flow" of solvent between the nascent ions, and the direct (dipolar?) interaction of solvent with the ions. Most physical organic books should have a discussion of solvent-separated reaction partners, and most likely SN1 reactions in particular. Cheers, Steve Wenrui Zheng wenruizheng:gmail.com wrote: > Sent to CCL by: "Wenrui Zheng" [wenruizheng..gmail.com] > > Dear all, > Recently I have failed to find the transition state of the first > step of solvolyses of alkyl halide RX,for example tert-Butylchloride > in methanol solvent by using Gaussian03. > RX->R+ + X- > Following the lengths of C-Cl increasing,the potential energy rises > all along,which is the same with the case of in methanol solvent by using PCM model. > > Now I have some questions: > 1. Can we on earth find the transition state of SN1 reaction by using Gaussian03? > > 2. Is traditional transition state theory adapt to any system for example this one ? > If it is true then how can this kind of reaction happen and how can we > calculate the reaction rate? > > Regards, > > Wenrui Zhenghttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Jul 17 10:14:01 2006 From: "andras.borosy]-[givaudan.com" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32157-060717095113-29150-Pta1e2IITl73tnqPI1HRBg_+_server.ccl.net> X-Original-From: andras.borosy|,|givaudan.com Content-Type: multipart/alternative; boundary="=_alternative 004BF3AAC12571AE_=" Date: Mon, 17 Jul 2006 15:49:35 +0200 MIME-Version: 1.0 Sent to CCL by: andras.borosy ~~ givaudan.com This is a multipart message in MIME format. --=_alternative 004BF3AAC12571AE_= Content-Type: text/plain; charset="ISO-8859-2" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Might anyone suggest me a good text book on molecular dynamics? Many thank in advance, Dr. Andr=E1s P=E9ter Borosy Senior Scientist Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-1-824 2164 - F:+41-1-8242926 - http://www.givaudan.com --=_alternative 004BF3AAC12571AE_= Content-Type: text/html; charset="ISO-8859-2" Content-Transfer-Encoding: quoted-printable
Dear Colleagues,

Might anyone suggest me a good text book on molecular dynamics?

Many thank in advance,

Dr. Andr=E1s P=E9ter Borosy
Senior Scientist
Fragrance Research
Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600  -  D=FCbendorf  -  Switzerland
T:+41-1-824 2164  -  F:+41-1-8242926    -  http://= www.givaudan.com
--=_alternative 004BF3AAC12571AE_=-- From owner-chemistry@ccl.net Mon Jul 17 10:48:01 2006 From: "Shobe, David dshobe * sud-chemieinc.com" To: CCL Subject: CCL:G: gaussian calculations Message-Id: <-32158-060717093424-27471-y0Qx374WvZhqnYuh6PX9Kg*server.ccl.net> X-Original-From: "Shobe, David" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Mon, 17 Jul 2006 15:34:12 +0200 MIME-Version: 1.0 Sent to CCL by: "Shobe, David" [dshobe[*]sud-chemieinc.com] What types of ab initio calculations can we perform on a reaction? 1. We can obtain Delta H, Delta S, and Delta G by calculating these thermodynamic functions for each reactant and product, separately. There are various methods for calculating these thermodynamic functions with reasonably high accuracy--CBS-4M, G3B3, G3(MP2), etc. 2. We can find the transition state of the reaction. This calculation will give you not only the energy of the transition state (which can be compared to the energy of the reatants to obtain the activation energy), and will also give you a "picture" of the transition state. The latter is actually a set of atomic (x,y,z) positions, but there are utilities which convert these coordiantes to an actual picture (graphic image). I'm sure there are others but those are the main types of calculations. I would advise finding a textbook on computational chemistry if you're planning on doing any calculations. You really cannot learn all you need to know from email alone. --David Shobe, Ph.D., M.L.S. Süd-Chemie, Inc. phone (502) 634-7409 fax (502) 634-7724 Don't bother flaming me: I'm behind a firewall. -----Original Message----- > From: owner-chemistry,,ccl.net [mailto:owner-chemistry,,ccl.net] Sent: Sunday, July 16, 2006 10:41 PM To: Shobe, David Subject: CCL: gaussian calculations Sent to CCL by: "Neeraj Misra" [misraneeraj-*-gmail.com] HOW CAN WE PERFORM AB INITIO CALCULATIONS (AND WHAT TYPE) ON A CHEMICAL REACTION.WHAT ARE THE POSSIBILITIES OF CALCULATIONS AND IMPORTANCE TOO. ANY HELP WOULD BE GREATLY ACKNOWLEDGED. THANKS IN ADVANCEhttp://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txtThis e-mail message may contain confidential and / or privileged information. If you are not an addressee or otherwise authorized to receive this message, you should not use, copy, disclose or take any action based on this e-mail or any information contained in the message. If you have received this material in error, please advise the sender immediately by reply e-mail and delete this message. Thank you. From owner-chemistry@ccl.net Mon Jul 17 11:23:00 2006 From: "Karl Irikura karl.irikura-#-nist.gov" To: CCL Subject: CCL:G: Normal mode displacement in GAUSSIAN Message-Id: <-32159-060714013904-31310-Pta1e2IITl73tnqPI1HRBg=server.ccl.net> X-Original-From: Karl Irikura Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Thu, 13 Jul 2006 09:23:11 -0400 Mime-Version: 1.0 Sent to CCL by: Karl Irikura [karl.irikura .. nist.gov] Hi. I believe the NMs in Gaussian are in units of distance (without mass weighting) and are normalized to 1 unit of distance. If that's correct, you need to add the mass weights and then renormalize to get "standard" NM vectors. I've forgotten what the red. mass is, but it's probably just the normalization factor. Good luck, Karl At 12:32 AM 7/13/2006, you wrote: >Sent to CCL by: "Hiro Maekawa" [hmaekawa!A!uci.edu] >Dear CCL, > >I have difficulty in understanding normal mode displacement obtained >from GAUSSIAN03 package. I have read a paper in the GAUSSIAN website >("vibrational analysis in GAUSSIAN") and checked the CCL archive, >but it is still not clear whether I am correct or not. > >I would like to get a matrix L which relates normal mode coordinate >Q [angstrom*(amu)1/2] and cartesian coordinate x [angstrom] of 3N >atoms, that is x=LQ. > >In the GAUSSIAN output file, you can get normal coordinate which >does not have any unit as follows. > > incident light, reduced masses (AMU), force constants (mDyne/A), > and normal coordinates: > Atom > AN X Y Z X Y Z X Y Z > 1 6 0.00 0.00 0.00 0.00 0.00 0.03 0.00 > 0.00 0.07 > 2 8 0.00 0.00 0.04 0.00 0.00 0.06 0.00 > 0.00 0.03 > 3 7 0.00 0.00 -0.06 0.00 0.00 0.00 0.00 > 0.00 0.30 > >My concerns are... >1. These displacements are normalized by multiplying by square root >of the reduced mass, and hence are dimensionless. I need to divide >by it to obtain the original numbers. > >2. The numbers I get after the process 1 are elements of the >trasposed matrix of L (=tL), that is Q=(tL)x. > >If these are wrong, please tell me the correct. >I appreciate your help. > >--------------------------------------- >Hiro Maekawa >hmaekawa###uci.edu >Rowland Hall, Irvine, USA.---------------------------------------------- Dr. Karl K. Irikura National Institute of Standards and Technology 100 Bureau Drive, Stop 8380 Gaithersburg, MD 20899-8380 voice: 301-975-2510 fax: 301-869-4020 e-mail: karl.irikura(a)nist.gov http://www.nist.gov/compchem/ ---------------------------------------------- From owner-chemistry@ccl.net Mon Jul 17 11:59:01 2006 From: "Sujata Guha sguha/a\tnstate.edu" To: CCL Subject: CCL: SecureCRT Message-Id: <-32160-060717111410-28145-eIMTeDLoMEiaNiKKd2vATw::server.ccl.net> X-Original-From: "Sujata Guha" Date: Mon, 17 Jul 2006 11:14:09 -0400 Sent to CCL by: "Sujata Guha" [sguha^_^tnstate.edu] Dear CCL Subscribers: Does anyone know of a free SecureCRT download (one that does not link you to the VanDyke website with their 30-day only trial period)? Any suggestions will be appreciated. Thanks. Sujata Guha, Ph.D. Assistant Professor of Chemistry Tennessee State University 3500 John Merritt Blvd. Nashville, TN 37209 U.S.A. Phone: (615)963-5334 Email: sguha(0)tnstate.edu From owner-chemistry@ccl.net Mon Jul 17 12:33:00 2006 From: "Jeff Nauss jnauss . accelrys.com" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32161-060717114919-12348-W/ppubOFzGqCeRMmUc0zQg=server.ccl.net> X-Original-From: Jeff Nauss Content-Type: multipart/alternative; boundary="=_alternative 0056E4C7882571AE_=" Date: Mon, 17 Jul 2006 08:48:52 -0700 MIME-Version: 1.0 Sent to CCL by: Jeff Nauss [jnauss:-:accelrys.com] This is a multipart message in MIME format. --=_alternative 0056E4C7882571AE_= Content-Type: text/plain; charset="US-ASCII" owner-chemistry _ ccl.net wrote on 07/17/2006 08:26:40 AM: > Might anyone suggest me a good text book on molecular dynamics? Here are four that I can personally recommend: Andrew R. Leach, Molecular Modelling: Principles & Applications, 2nd Edition, Prentice Hall, 2001 M.P. Allen and D.J. Tidesley, Computer Simulation of Liquids, Oxford Science Publications, Oxford, 1989 J. M. Haile, Molecular Dynamics Simulation: Elementary Methods. John Wiley & Sons, Inc. , New York, 1992 D.C. Rapaport, The Art of Molecular Dynamics Simulations, Cambridge University Press, 1995 While I cannot personally attest to the book, I also have heard good things about: Understanding Molecular Simulation by Daan Frenkel, B. Smit (2001) Jeff -- Jeffrey L. Nauss, Ph.D. Lead Training Scientist Accelrys 10188 Telesis Court, Suite 100 San Diego, CA 92121-4779 Phone: +1-858-799-5555 Fax: +1-858-799-5100 http://www.accelrys.com/training --=_alternative 0056E4C7882571AE_= Content-Type: text/html; charset="US-ASCII"
owner-chemistry _ ccl.net wrote on 07/17/2006 08:26:40 AM:

> Might anyone suggest me a good text book on molecular dynamics?
Here are four that I can personally recommend:

     Andrew R. Leach, Molecular Modelling: Principles & Applications, 2nd Edition, Prentice Hall, 2001
     M.P. Allen and D.J. Tidesley, Computer Simulation of Liquids, Oxford Science Publications, Oxford, 1989
     J. M. Haile, Molecular Dynamics Simulation: Elementary Methods. John Wiley & Sons, Inc. , New York, 1992
     D.C. Rapaport, The Art of Molecular Dynamics Simulations, Cambridge University Press, 1995

While I cannot personally attest to the book, I also have heard good things about:

     Understanding Molecular Simulation by Daan Frenkel, B. Smit (2001)

Jeff
--
Jeffrey L. Nauss, Ph.D.
Lead Training Scientist
Accelrys
10188 Telesis Court, Suite 100
San Diego, CA 92121-4779

Phone: +1-858-799-5555
Fax: +1-858-799-5100
http://www.accelrys.com/training
 --=_alternative 0056E4C7882571AE_=-- From owner-chemistry@ccl.net Mon Jul 17 13:18:01 2006 From: "Loan Huynh huynhkl2000]_[yahoo.ca" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32162-060717123539-15793-DhvkCYMZPYuc+pChcLNVDw.:.server.ccl.net> X-Original-From: Loan Huynh Content-Transfer-Encoding: 8bit Content-Type: multipart/alternative; boundary="0-2070764703-1153150529=:78541" Date: Mon, 17 Jul 2006 11:35:29 -0400 (EDT) MIME-Version: 1.0 Sent to CCL by: Loan Huynh [huynhkl2000*_*yahoo.ca] --0-2070764703-1153150529=:78541 Content-Type: text/plain; charset=iso-8859-1 Content-Transfer-Encoding: 8bit Hi Andras, This book is a good one on MD: M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids. Oxford University Press, New York, 1987. Cheers, "andras.borosy]-[givaudan.com" wrote: Sent to CCL by: andras.borosy ~~ givaudan.com This is a multipart message in MIME format. --=_alternative 004BF3AAC12571AE_= Content-Type: text/plain; charset="ISO-8859-2" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Might anyone suggest me a good text book on molecular dynamics? Many thank in advance, Dr. Andr=E1s P=E9ter Borosy Senior Scientist Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= =20 Switzerland T:+41-1-824 2164 - F:+41-1-8242926 - http://www.givaudan.com --=_alternative 004BF3AAC12571AE_= Content-Type: text/html; charset="ISO-8859-2" Content-Transfer-Encoding: quoted-printable Dear Colleagues, Might anyone suggest me a good text book on molecular dynamics? Many thank in advance, Dr. Andr=E1s P=E9ter Borosy Senior Scientist Fragrance Research Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf - Switzerland T:+41-1-824 2164 - F:+41-1-8242926 - http://= www.givaudan.com --=_alternative 004BF3AAC12571AE_=--http://www.ccl.net/cgi-bin/ccl/send_ccl_messagehttp://www.ccl.net/chemistry/sub_unsub.shtmlhttp://www.ccl.net/spammers.txt--0-2070764703-1153150529=:78541 Content-Type: text/html; charset=iso-8859-1 Content-Transfer-Encoding: 8bit
Hi Andras,
 
This book is a good one on MD:
 
M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids. Oxford University Press, New York, 1987.
 
Cheers,

"andras.borosy]-[givaudan.com" <owner-chemistry-,-ccl.net> wrote:
Sent to CCL by: andras.borosy ~~ givaudan.com
This is a multipart message in MIME format.
--=_alternative 004BF3AAC12571AE_=
Content-Type: text/plain; charset="ISO-8859-2"
Content-Transfer-Encoding: quoted-printable

Dear Colleagues,

Might anyone suggest me a good text book on molecular dynamics?

Many thank in advance,

Dr. Andr=E1s P=E9ter Borosy
Senior Scientist
Fragrance Research
Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -=
=20
Switzerland
T:+41-1-824 2164 - F:+41-1-8242926 - http://www.givaudan.com

--=_alternative 004BF3AAC12571AE_=
Content-Type: text/html; charset="ISO-8859-2"
Content-Transfer-Encoding: quoted-printable



Dear Colleagues,



Might anyone suggest me a good text
book on molecular dynamics?



Many thank in advance,



Dr. Andr=E1s P=E9ter Borosy

Senior Scientist

Fragrance Research

Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600
 -  D=FCbendorf  -  Switzerland

T:+41-1-824 2164  -  F:+41-1-8242926    -  http://=
www.givaudan.com


--=_alternative 004BF3AAC12571AE_=--


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--0-2070764703-1153150529=:78541-- From owner-chemistry@ccl.net Mon Jul 17 13:52:00 2006 From: "Raymond C. Fort Jr. rcfort[A]maine.edu" To: CCL Subject: CCL: SecureCRT Message-Id: <-32163-060717131721-2665-xCzvlNjqCAJllThp2gFCwA|a|server.ccl.net> X-Original-From: "Raymond C. Fort Jr." Content-Type: text/plain; charset="us-ascii"; format=flowed Date: Mon, 17 Jul 2006 12:37:00 -0400 Mime-Version: 1.0 Sent to CCL by: "Raymond C. Fort Jr." [rcfort,+,maine.edu] At 12:11 PM 7/17/2006 -0400, you wrote: >Sent to CCL by: "Sujata Guha" [sguha^_^tnstate.edu] >Dear CCL Subscribers: > >Does anyone know of a free SecureCRT download (one that does not link you >to the VanDyke website with their 30-day only trial period)? Any >suggestions will be appreciated. Thanks. > >Sujata Guha, Ph.D. >Assistant Professor of Chemistry >Tennessee State University >3500 John Merritt Blvd. >Nashville, TN 37209 >U.S.A. >Phone: (615)963-5334 >Email: sguha-#-tnstate.edu CRT is, of course, VanDyke's program, developed by them and available from them. If what you want is a secure telnet, try Putty http://www.chiark.greenend.org.uk/~sgtatham/putty/ which is free.Professor Ray Fort Jr. rcfort:_:maine.edu Department of Chemistry chemistry.umeche.maine.edu/fort.html University of Maine Voice: (207)-581-1180 Orono, ME 04469 FAX: (207)-581-1191 Computer modeling of organic and biomolecules; chemistry of lignin and cellulose From owner-chemistry@ccl.net Mon Jul 17 14:46:00 2006 From: "David F. Green dfgreen!A!ams.sunysb.edu" To: CCL Subject: CCL: SecureCRT Message-Id: <-32164-060717144223-13176-1YqYHK+1Y694T8tyZJ7QZg*server.ccl.net> X-Original-From: "David F. Green" Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Jul 2006 13:14:18 -0400 MIME-Version: 1.0 Sent to CCL by: "David F. Green" [dfgreen*ams.sunysb.edu] Since SecureCRT is not free software, perhaps looking for a free download site isn't the best way to go. However, there are free alternatives for SSH on Windows. PuTTY (http://www.putty.nl/) works nicely, but of course you will need an X-windows client if you want more than just terminal access. X-forwarding works fine if you do, though. Cygwin (http://www.cygwin.com/) provides a Linux-like environment under Windows. As such, you get ssh, and can also install an X-server/client. Cygwin/X also works perfectly fine as the X-client side of things if you choose an alternative SSH-client (such as PuTTY). ======================================================================= David F. Green Assistant Professor http://www.ams.sunysb.edu/~dfgreen/ Applied Mathematics and Statistics Stony Brook University Math Tower, Room 1-117 Voice: +1-631-632-9344 Stony Brook, NY 11794-3600 Fax: +1-631-632-8490 ======================================================================= Sujata Guha sguha/atnstate.edu wrote: > Sent to CCL by: "Sujata Guha" [sguha^_^tnstate.edu] > Dear CCL Subscribers: > > Does anyone know of a free SecureCRT download (one that does not link you to the VanDyke website with their 30-day only trial period)? Any suggestions will be appreciated. Thanks. > > Sujata Guha, Ph.D. > Assistant Professor of Chemistry > Tennessee State University > 3500 John Merritt Blvd. > Nashville, TN 37209 > U.S.A. > Phone: (615)963-5334 > Email: sguha-#-tnstate.edu> > > From owner-chemistry@ccl.net Mon Jul 17 15:55:01 2006 From: "John Daily john.daily]-[colorado.edu" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32166-060717141928-3888-0AQh6FE/YKWOvV8XugobHA.:.server.ccl.net> X-Original-From: John Daily Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed Date: Mon, 17 Jul 2006 11:40:35 -0600 Mime-Version: 1.0 (Apple Message framework v752.2) Sent to CCL by: John Daily [john.daily*|*colorado.edu] "Essentials of Computational Chemistry: Theories and Models," 2nd Edition by C. J. Cramer, Wiley Reprinted with corrections 2006. On Jul 17, 2006, at 11:09 AM, andras.borosy]-[givaudan.com wrote: > Sent to CCL by: andras.borosy ~~ givaudan.com > This is a multipart message in MIME format. > --=_alternative 004BF3AAC12571AE_= > Content-Type: text/plain; charset="ISO-8859-2" > Content-Transfer-Encoding: quoted-printable > > Dear Colleagues, > > Might anyone suggest me a good text book on molecular dynamics? > > Many thank in advance, > > Dr. Andr=E1s P=E9ter Borosy > Senior Scientist > Fragrance Research > Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - > D=FCbendorf -= > =20 > Switzerland > T:+41-1-824 2164 - F:+41-1-8242926 - http://www.givaudan.com > > --=_alternative 004BF3AAC12571AE_= > Content-Type: text/html; charset="ISO-8859-2" > Content-Transfer-Encoding: quoted-printable > > >
Dear Colleagues, >
>
Might anyone suggest me a > good text > book on molecular dynamics? >
>
Many thank in advance, >

> Dr. Andr=E1s P=E9ter Borosy
> Senior Scientist
> Fragrance Research
> Givaudan Schweiz AG  -  Ueberlandstrasse 138  - >  CH-8600 >  -  D=FCbendorf  -  Switzerland
> T:+41-1-824 2164  -  F:+41-1-8242926    - >  http://= > www.givaudan.com >
> --=_alternative 004BF3AAC12571AE_=-- > > > > -= This is automatically added to each message by the mailing > script =- > To recover the email address of the author of the message, please > change> Conferences: http://server.ccl.net/chemistry/announcements/ > conferences/ > > Search Messages: http://www.ccl.net/htdig (login: ccl, Password: > search)> > -+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+- > +-+-+ > > From owner-chemistry@ccl.net Mon Jul 17 15:20:01 2006 From: "Anselm.Horn%%chemie.uni-erlangen.de" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32165-060717150550-5809-YCv88VTjz2c3y7n2pwhYDA**server.ccl.net> X-Original-From: Anselm.Horn{=}chemie.uni-erlangen.de Content-Transfer-Encoding: 8bit Content-Type: text/plain;charset=iso-8859-1 Date: Mon, 17 Jul 2006 21:05:25 +0200 (CEST) MIME-Version: 1.0 Sent to CCL by: Anselm.Horn*chemie.uni-erlangen.de Hi Andreas, if you have access to Charmm (and ideally InsightII and Quanta) then the "Guide to Biomolecular Simulations" (Springer, 2006) by Becker & Karplus might be a good workbook for you. Regards, Anselm From owner-chemistry@ccl.net Mon Jul 17 16:32:01 2006 From: "Lukasz Cwiklik lukasz.cwiklik/./uochb.cas.cz" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32167-060717135500-28254-rW+QlYck/HbnMt09QKmgFg||server.ccl.net> X-Original-From: "Lukasz Cwiklik" Content-Disposition: inline Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 17 Jul 2006 18:32:45 +0200 MIME-Version: 1.0 Sent to CCL by: "Lukasz Cwiklik" [lukasz.cwiklik[]uochb.cas.cz] On 7/17/06, andras.borosy]-[givaudan.com wrote: > Dear Colleagues, > > Might anyone suggest me a good text book on molecular dynamics? Hi, I suggest "Computer simulations of liquids" by Allen and Tildesley. It is a good introduction for MD (and Monte Carlo), including both general chapters and implementation details (even some source codes). Best regards, Lukasz Cwiklik -- Lukasz Cwiklik http://www.molecular.cz/~cwiklik From owner-chemistry@ccl.net Mon Jul 17 17:35:01 2006 From: "Rick Venable rvenable-$-pollux.cber.nih.gov" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32168-060717153735-19829-lky+hEg5/08k3IUVy/1BDw(0)server.ccl.net> X-Original-From: Rick Venable Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Mon, 17 Jul 2006 14:02:30 -0400 MIME-Version: 1.0 Sent to CCL by: Rick Venable [rvenable-x-pollux.cber.nih.gov] On Mon, 17 Jul 2006, andras.borosy]-[givaudan.com wrote: > Might anyone suggest me a good text book on molecular dynamics? Computer Simulation of Liquids MP Allen, DJ Tildesley Oxford Univ. Press; New York, London ISBN 0-19-855375-7 hardcover ISBN 0-19-855645-4 paperbook Molecular Modelling: Principles and Applications Andrew R Leach Pearson Education Ltd.; Essex, England ISBN 0-582-23933-8 A Practical Introduction to the Simulation of Molecular Systems Martin J Field Cambridge Univ. Press; Cambridge UK, New York, Melbourne ISBN 0-521-58129-X ------------------------------------- Rick Venable 29/500 Membrane Biophysics Section NIH/NHLBI Lab. of Comp. Biology Bethesda, MD 20892-8014 U.S.A. (301) 496-1905 Rick_Venable AT nih*gov ALT email: rvenable AT speakeasy*org ------------------------------------- From owner-chemistry@ccl.net Mon Jul 17 20:35:01 2006 From: "Fernando D. Vila fer#%#phys.washington.edu" To: CCL Subject: CCL: Solvation of organic molecules (with GROMACS) Message-Id: <-32169-060717202537-10433-/OPCiZJpfbZAuHI1LWn7lQ * server.ccl.net> X-Original-From: "Fernando D. Vila" Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed Date: Mon, 17 Jul 2006 15:54:58 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "Fernando D. Vila" [fer ~~ phys.washington.edu] Hello everyone.. A summer student and I are trying to simulate the solvation of some organic molecules. What we want is something that is very black-box: we give it a molecule, a solvent, we choose a force field, set up some MD parameters and we running. I'm sure there is a solution "out there", it looks like a pretty easy problem. We don't need anything very sophisticated since we are just trying to generate some MD snapshots to use in explicit solvent ab initio calculations of UV-Vis spectra (we just want to check a couple of ideas). He downloaded GROMACS and got it running. The problem he run into is that, although it is very easy to generate inputs for solvated ions and solvated polypeptides, it isn't very clear how to generate them for an arbitrary organic molecule like, say, benzene or aniline. I'm willing to drop GROMACS if anyone thinks there is an easier solution. Any suggestions will be quite welcome. Best regards, Fer. Ubi dubium ibi libertas. ******************************************************************************* Fernando D. Vila Voice (206)543-9697 Department of Physics Fax (206)685-0635 University of Washington E-mail fdv~!~u.washington.edu Seattle, WA 98195, USA WWW http://faculty.washington.edu/fdv ******************************************************************************* From owner-chemistry@ccl.net Mon Jul 17 22:26:00 2006 From: "=?windows-1252?Q?Carlos_Javier_Nu=F1ez_Aguero?= carlosjn]=[ce.fis.unam.mx" To: CCL Subject: CCL: Text book on MD? Message-Id: <-32170-060717220958-5401-xMAc073BLlt/JhQDcnp/Gw]~[server.ccl.net> X-Original-From: =?windows-1252?Q?Carlos_Javier_Nu=F1ez_Aguero?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=windows-1252; format=flowed Date: Mon, 17 Jul 2006 20:18:47 -0500 Mime-Version: 1.0 Sent to CCL by: =?windows-1252?Q?Carlos_Javier_Nu=F1ez_Aguero?= [carlosjn(a)ce.fis.unam.mx] Hi all, You might find useful the next book: o Computational Biochemistry & Biophysics Oren M. Becker, Alexander D. MacKerell, Jr.; Benoit Roux & Masakatsu Watanabe Eds. Dekker Books From the website: "This comprehensive reference/text presents the most recent theoretical methods and computational techniques in biomolecular research—focusing on a variety of approaches for the treatment of macromolecules, including proteins, nucleic acids, and bilayer membranes. Furnishing essential concepts in free energy calculations, conformational analysis, reaction rates and transition pathways." Regards, Carlos J. Nuñez A. andras.borosy]-[givaudan.com wrote: >Sent to CCL by: andras.borosy ~~ givaudan.com >This is a multipart message in MIME format. >--=_alternative 004BF3AAC12571AE_= >Content-Type: text/plain; charset="ISO-8859-2" >Content-Transfer-Encoding: quoted-printable > >Dear Colleagues, > >Might anyone suggest me a good text book on molecular dynamics? > >Many thank in advance, > >Dr. Andr=E1s P=E9ter Borosy >Senior Scientist >Fragrance Research >Givaudan Schweiz AG - Ueberlandstrasse 138 - CH-8600 - D=FCbendorf -= >=20 >Switzerland >T:+41-1-824 2164 - F:+41-1-8242926 - http://www.givaudan.com > >--=_alternative 004BF3AAC12571AE_= >Content-Type: text/html; charset="ISO-8859-2" >Content-Transfer-Encoding: quoted-printable > > >
Dear Colleagues, >
>
Might anyone suggest me a good text >book on molecular dynamics? >
>
Many thank in advance, >

>Dr. Andr=E1s P=E9ter Borosy
>Senior Scientist
>Fragrance Research
>Givaudan Schweiz AG  -  Ueberlandstrasse 138  -  CH-8600 > -  D=FCbendorf  -  Switzerland
>T:+41-1-824 2164  -  F:+41-1-8242926    -  http://= >www.givaudan.com >
>--=_alternative 004BF3AAC12571AE_=--> > > > > > -- No virus found in this outgoing message. Checked by AVG Free Edition. Version: 7.1.394 / Virus Database: 268.10.1/389 - Release Date: 7/14/2006