From owner-chemistry@ccl.net Wed Aug 16 03:11:01 2006 From: "neeraj misra misraneeraj#gmail.com" To: CCL Subject: CCL:G: assignments in vibrational frequency output Message-Id: <-32393-060816030847-20510-peijPlaOKHMmUHtwjNbSiw * server.ccl.net> X-Original-From: "neeraj misra" Date: Wed, 16 Aug 2006 03:08:47 -0400 Sent to CCL by: "neeraj misra" [misraneeraj||gmail.com] Dear ccl'ers, I would be grateful if someone of you could advise me how to pick up the assignments (potential energy distributions) in the vibrational analysis output of a gaussian 03 W run.I have done the vibrational analysis but how to know that which mode (i.e stretch, angle bend, wag, torsion) is having significant contribution at a particular frequency.Anyone who can explain with a gaussian vibrational freq example would be a big help.I realise its a trivial question but it does matter to someone like me. thanks in advance neeeraj From owner-chemistry@ccl.net Wed Aug 16 09:34:01 2006 From: "Ozgur Yazaydin yazaydin+*+wpi.edu" To: CCL Subject: CCL: 9-6 Lennard-Jones water potential Message-Id: <-32394-060816090136-16387-ht0dyurEnJR2VyPJHQunJw**server.ccl.net> X-Original-From: "Ozgur Yazaydin" Date: Wed, 16 Aug 2006 09:01:35 -0400 Sent to CCL by: "Ozgur Yazaydin" [yazaydin(a)wpi.edu] Dear all, Does anybody know a water model published in the open literature with a 9-6 Lennard-Jones type potential? Thanks -- Ozgur YAZAYDIN Department of Chemical Engineering Worcester Polytechnic Institute 100 Institute Rd. Worcester, MA 01609-2280 USA From owner-chemistry@ccl.net Wed Aug 16 11:49:00 2006 From: "Jun Zhao jzhao*tamu.edu" To: CCL Subject: CCL: How to otain Gibbs free energy for formation of a cluster? Message-Id: <-32395-060816114630-28924-CHX/7O48sygNDgN7PGo5Bg]|[server.ccl.net> X-Original-From: "Jun Zhao" Date: Wed, 16 Aug 2006 11:46:30 -0400 Sent to CCL by: "Jun Zhao" [jzhao(0)tamu.edu] Hi,Dear cclers, First I want to express my sincere thanks to all the people who teach me how to prepare a simulation movie in my previous poster. My next question is: does anyone know how to get Gibbs free energy for formation of a cluster from molecular dynamic simulation? The cluster is formed from 3 components of molecules. Its size is around 25 molecules. I used cerius2 OFF to do the simulation. I wonder if it is possible to get the Gibbs free energy for formation of such a cluster. If yes, what kind of simulation engine and method I should use. Thanks a lot. Jun From owner-chemistry@ccl.net Wed Aug 16 13:52:00 2006 From: "Schrodinger Announcements announce..schrodinger.com" To: CCL Subject: CCL: MacroModel celebration at Fall ACS Message-Id: <-32396-060816135008-26000-e0bbGLKrn23UXjA0A+gljw%x%server.ccl.net> X-Original-From: "Schrodinger Announcements" Date: Wed, 16 Aug 2006 13:50:08 -0400 Sent to CCL by: "Schrodinger Announcements" [announce##schrodinger.com] Come join us in celebrating MacroModel's 20th anniversary at the upcoming ACS meeting in San Francisco. A special symposium is being held on Thursday, September 14th, from 9AM to noon, in Room 125 of the Moscone Center. Continental breakfast and coffee break refreshments will be served. Come meet other users, product managers and developers and learn about the innovative ways MacroModel is being used to address current problems in computational chemistry, as well as current and future directions in product development. We would also like to hear about your own MacroModel applications, so please contact me directly (jshelley : schrodinger.com) with a title and short abstract if you are interested in sharing your research story. Hope to see you there, John Shelley, Ph.D. MacroModel Product Manager jshelley : schrodinger.com From owner-chemistry@ccl.net Wed Aug 16 15:54:01 2006 From: "Alejandro Arzate Jacinto aarzate[]nucleares.unam.mx" To: CCL Subject: CCL:G: How to install gaussian 03 with Linda in a cluster with O.S.Rocks 4.1? Message-Id: <-32397-060816131659-23368-WoMYcoEwn/qIriXhAHGkhg+*+server.ccl.net> X-Original-From: "Alejandro Arzate Jacinto" Date: Wed, 16 Aug 2006 13:16:58 -0400 Sent to CCL by: "Alejandro Arzate Jacinto" [aarzate]_[nucleares.unam.mx] Hi,Dear cclers, my name is Alejandro and I am new user of the list. The motivation that I have registered myself for to the list is why in the working group where I am we have constructed a cluster with 11 CPU's Pentium IV , these have installed Linux Rocks 4.1 and gaussian 03. My first question for you is : does somebody know like to install and configuring gaussian 03 in order that it work in parallel? As he right now mention we have installed 11 CPU's, S.O. Rocks Linux 4.1 and gaussian 03, however, I could have done 03 with Linda than gaussian 03, run in tandem. Hoping that somebody may help me. Thanks a lot. From owner-chemistry@ccl.net Wed Aug 16 16:29:00 2006 From: "Alejandro Arzate Jacinto. aarzate*nucleares.unam.mx" To: CCL Subject: CCL:G: How to install gaussian 03 with Linda in a cluster with operating system Linux Rocks 4.1? Message-Id: <-32398-060816132651-24216-3RpsV2yi+fftzOctASjPbg^server.ccl.net> X-Original-From: "Alejandro Arzate Jacinto." Content-Type: multipart/alternative; boundary="----=_Part_205833_8796815.1155748675806" Date: Wed, 16 Aug 2006 12:17:55 -0500 MIME-Version: 1.0 Sent to CCL by: "Alejandro Arzate Jacinto." [aarzate(0)nucleares.unam.mx] ------=_Part_205833_8796815.1155748675806 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi,Dear cclers, my name is Alejandro and I am new user of the list. The motivation that I have registered myself for to the list is why in the working group where I am we have constructed a cluster with 11 CPU's Pentiu= m IV , these have installed Linux Rocks 4.1 and gaussian 03. My first questio= n for you is : does somebody know like to install and configuring gaussian 03 in order tha= t it work in parallel? As he right now mention we have installed 11 CPU's, S.= O. Rocks Linux 4.1 and gaussian 03, however, I could have done 03 with Linda than gaussian 03, run in tandem. Hoping that somebody may help me. Thanks a lot. Salu2 AleXtremo --=20 y recuerda *************************************************************** =A1Que una estrella brille a la hora de nuestro encuentro! Salu2 AleXtremo ------=_Part_205833_8796815.1155748675806 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Content-Disposition: inline Hi,Dear cclers, my name is Alejandro and I am new user of the list. The mot= ivation that I have registered  myself  for to the list is why in= the working group where I am we have constructed a cluster with 11 CPU's P= entium IV , these have installed Linux Rocks=20 4.1 and gaussian 03. My first question for you is :

does someb= ody know like to install and configuring gaussian 03 in order that it work = in parallel? As he right now mention we have installed 11 CPU's, S.O. Rocks= Linux=20 4.1 and gaussian 03, however, I could have done 03 with Linda than gaussian= 03, run in tandem.

Hoping that somebody may help me.

Thanks = a lot.



   Salu2
AleXtremo


--
y recuerda
**************************= *************************************
=A1Que una estrella brille a la ho= ra de nuestro encuentro!

   Salu2
AleXtremo ------=_Part_205833_8796815.1155748675806-- From owner-chemistry@ccl.net Wed Aug 16 21:23:01 2006 From: "S.I.Gorelsky gorelsky]|[stanford.edu" To: CCL Subject: CCL: updated version of AOMix-CDA is available Message-Id: <-32399-060816212156-14002-JzBuRS5Ru5KE5tbV9MHSfQ++server.ccl.net> X-Original-From: "S.I.Gorelsky" Content-Type: TEXT/PLAIN; charset=US-ASCII Date: Wed, 16 Aug 2006 18:21:43 -0700 (PDT) MIME-Version: 1.0 Sent to CCL by: "S.I.Gorelsky" [gorelsky()stanford.edu] Hello, the updated version of AOMix-CDA (revision 2.02) is available for downloading at http://www.sg-chem.net The new functionality includes the ability to generate guess wave functions of multi-fragment molecular systems using the wave functions of the fragments. This should be especially helpful for generating correct spin state for open-shell broken symmetry and low-spin, anti-ferromagnetically coupled systems. For detailes, please refer to the AOMix manual (http://www.sg-chem.net/aomix/AOMix-manual.pdf) With best regards, Serge Gorelsky ----------------------------------------------------------------- Dr. S.I. Gorelsky, Department of Chemistry, Stanford University Box 155, 333 Campus Drive, Stanford, CA 94305-5080 USA Fax: (650) 960-3912 -----------------------------------------------------------------