From owner-chemistry@ccl.net Thu Aug 12 00:44:01 2010 From: "sudipta sudipta.mml===gmail.com" To: CCL Subject: CCL: Calculation of enthalpy from NPT simulation Message-Id: <-42510-100811145730-1133-jmWJBst3ye/jFmrLqtmOOQ_._server.ccl.net> X-Original-From: sudipta Content-Type: multipart/alternative; boundary=0016e68ce6f2e9631d048d90d139 Date: Thu, 12 Aug 2010 00:27:23 +0530 MIME-Version: 1.0 Sent to CCL by: sudipta [sudipta.mml{:}gmail.com] --0016e68ce6f2e9631d048d90d139 Content-Type: text/plain; charset=ISO-8859-1 Hi All, I have ran a NPT simulation for a liquid water system (TIP3P) model by NAMD package and want to calculate enthalpy of the system at that temperature. How shall I proceed? I have used lagevin dynamics for temperature and pressure control. As I know the conserved quantity in NPT ensemble is enthalpy. In the output file of the simulation it provides kinetic energy and potential energy of the system. But the kinetic and potential energy of extended part is not given their. How shall I extract them from a output file. If I calculate enthalpy as KE+PE+Pressure(ext)XdeltaV, then is it logical. The Pressure(ext) is the external pressure and deltaV is the volume change that given in .xst file. Any suggestion will be highly appreciated. Thanks and regards Sudipta --0016e68ce6f2e9631d048d90d139 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Hi All,
=A0=A0=A0=A0=A0=A0
=A0=A0=A0=A0=A0=A0=A0 I have ran a NPT simulation for a liquid water system= (TIP3P) model by NAMD package and want to calculate enthalpy of the system at that = temperature. How shall I proceed? I have used lagevin dynamics for temperature and pressure control. As I know the conserved quantity in NPT ensemble is enthalpy. In the output file of the simulation it provides kinetic energy and potential energy of the system. But the kinetic and potential energy of extended part is not given their. How shall I extract them from a output file.

If I calculate enthalpy as KE+PE+Pressure(ext)XdeltaV, then is it logical. The Pressure(ext) is the external pressure and deltaV is the volume change that given in .xst file.

Any suggestion will be highly appreciated.

Thanks and regards
Sudipta --0016e68ce6f2e9631d048d90d139-- From owner-chemistry@ccl.net Thu Aug 12 08:28:00 2010 From: "neeraj m neerajmisra:+:hotmail.com" To: CCL Subject: CCL: calculation Message-Id: <-42511-100812082654-19913-75ebEpd6uPUe0w/xVHY//g-x-server.ccl.net> X-Original-From: "neeraj m" Date: Thu, 12 Aug 2010 08:26:52 -0400 Sent to CCL by: "neeraj m" [neerajmisra{:}hotmail.com] HOW TO CALCULATE MAGNETIC MOMENT OF A NANOCLUSTER? From owner-chemistry@ccl.net Thu Aug 12 09:54:01 2010 From: "Prasenjit SEAL prasenjit.seal_._crm2.uhp-nancy.fr" To: CCL Subject: CCL:G: Problem in determining the emission maxima using Gaussian 03 Message-Id: <-42512-100812082532-18085-wXyCtGP3xji3lkSM5J/xXA[-]server.ccl.net> X-Original-From: Prasenjit SEAL Content-Type: multipart/alternative; boundary="------------060607090306070101010302" Date: Thu, 12 Aug 2010 14:25:23 +0200 MIME-Version: 1.0 Sent to CCL by: Prasenjit SEAL [prasenjit.seal[a]crm2.uhp-nancy.fr] This is a multi-part message in MIME format. --------------060607090306070101010302 Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 8bit Dear CCL users, Can anyone help me how to find the emission maxima using _Gaussian 03_ ? Thanks in advance, Prasenjit -- Prasenjit Seal Post-Doctoral Research Fellow CRM2 Universit Henri Poincar - Nancy I B.P. 239 F-54506 Vandoeuvre-les-Nancy, France --------------060607090306070101010302 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: 7bit Dear CCL users,

Can anyone help me how to find the emission maxima using Gaussian 03 ?

Thanks in advance,

Prasenjit
-- 
Prasenjit Seal
Post-Doctoral Research Fellow
CRM2
Université Henri Poincaré - Nancy I
B.P. 239
F-54506 Vandoeuvre-les-Nancy, France
--------------060607090306070101010302-- From owner-chemistry@ccl.net Thu Aug 12 10:47:01 2010 From: "John McKelvey jmmckel- -gmail.com" To: CCL Subject: CCL: Basis set notation Message-Id: <-42513-100812103233-31617-iuDx584H1PjfQPE3ZDf2wA**server.ccl.net> X-Original-From: John McKelvey Content-Type: text/plain; charset=ISO-8859-1 Date: Thu, 12 Aug 2010 10:32:26 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel|a|gmail.com] I may be out of touch on this: I take the basis set notation 6-31G(d,p) to be the same as 6-31G**. The question is whether or not the notation 6-31G(d',p' ) is accepted as an alternative for 6-31++G**, or is (d',p') a notation I'm just out of touch on? Thanks! John -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel_._gmail.com From owner-chemistry@ccl.net Thu Aug 12 12:44:00 2010 From: "Kirk Peterson kipeters:+:wsu.edu" To: CCL Subject: CCL: Basis set notation Message-Id: <-42514-100812123802-13744-53+o1hVeJM2XQqPXhbeUug[A]server.ccl.net> X-Original-From: Kirk Peterson Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 12 Aug 2010 09:37:24 -0700 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Kirk Peterson [kipeters{=}wsu.edu] John, I have never seen the notation (d',p') as an alias for ++G** and in my opinion it should be discouraged. It's bad enough that (d,p) is used instead of ** (although I know this is somewhat common practice). regards, Kirk ------------------------- Kirk A. Peterson Professor of Chemistry Department of Chemistry Washington State University Pullman, WA 99164-4630 office: (509) 335-7867 fax : (509) 335-8867 email: kipeters]_[wsu.edu web: http://tyr0.chem.wsu.edu/~kipeters/ On Aug 12, 2010, at 7:32 AM, John McKelvey jmmckel- -gmail.com wrote: > > Sent to CCL by: John McKelvey [jmmckel|a|gmail.com] > I may be out of touch on this: > > I take the basis set notation 6-31G(d,p) to be the same as 6-31G**. > The question is whether or not the notation 6-31G(d',p' ) is accepted > as an alternative for 6-31++G**, or is (d',p') a notation I'm just out > of touch on? > > Thanks! > > John > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel-#-gmail.com> > From owner-chemistry@ccl.net Thu Aug 12 13:40:01 2010 From: "Marcel Swart marcel.swart(a)icrea.es" To: CCL Subject: CCL: Basis set notation Message-Id: <-42515-100812133805-18449-ICFS+f7TlHn7g9ojR/Otow#server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=iso-8859-1 Date: Thu, 12 Aug 2010 19:37:57 +0200 Mime-Version: 1.0 (Apple Message framework v1081) Sent to CCL by: Marcel Swart [marcel.swart()icrea.es] I think the notation (d,p) is better suited than ** because it allows for extension to (2d,3p) or whatever other combination. The alternative in ** language would then be ***** ? Without making it clear that double polarized basis could also be used (2df, 3pd), etc. Marcel. On Aug 12, 2010, at 6:37 PM, Kirk Peterson kipeters:+:wsu.edu wrote: > John, > > I have never seen the notation (d',p') as an alias for ++G** and in my opinion it should > be discouraged. It's bad enough that (d,p) is used instead of ** (although I know this is > somewhat common practice). > > regards, > > Kirk > > ------------------------- > Kirk A. Peterson > Professor of Chemistry > Department of Chemistry > Washington State University > Pullman, WA 99164-4630 =================================== dr. Marcel Swart ICREA Research Professor at Institut de Qumica Computacional Universitat de Girona Parc Cientfic i Tecnolgic 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.marcelswart.eu =================================== From owner-chemistry@ccl.net Thu Aug 12 14:15:01 2010 From: "Cuperlovic-Culf, Miroslava Miroslava.Cuperlovic-Culf]=[nrc-cnrc.gc.ca" To: CCL Subject: CCL: Software(s) for molecule modelling, QM/MM and QM Message-Id: <-42516-100812123030-9666-MXttaBrSQBN0/JG4ts4VBg::server.ccl.net> X-Original-From: "Cuperlovic-Culf, Miroslava" Content-Language: en-US Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 12 Aug 2010 12:30:22 -0400 MIME-Version: 1.0 Sent to CCL by: "Cuperlovic-Culf, Miroslava" [Miroslava.Cuperlovic-Culf*nrc-cnrc.gc.ca] Dear All, We are considering setting up a computational chemistry facility. The primary interest would be in life sciences and would include steps for enhancing the drug discovery process including: Macromolecule modeling (proteins, RNA/DNA, lipids); small molecule (drug) modeling; docking; interaction simulations I have my opinions on what would be the best but as I am a bit out of data on these tools I would very much appreciate the opinions of all of you. We would like to optimize in terms of quality of calculations/user friendliness/price (in that order). You opinions/suggestions/experiences would be greatly appreciated. I will compile the answers subsequently for the benefit of the whole group, Sincerely, Mira Cuperlovic-Culf NRC, Canada From owner-chemistry@ccl.net Thu Aug 12 14:50:01 2010 From: "John L Kulp jlk287*nyu.edu" To: CCL Subject: CCL: new experimental solvation data Message-Id: <-42517-100812135246-833-59G+DNnuzv/WVZ3Bmt9D9A-#-server.ccl.net> X-Original-From: "John L Kulp" Date: Thu, 12 Aug 2010 13:52:40 -0400 Sent to CCL by: "John L Kulp" [jlk287]^[nyu.edu] Hello, What are the best references for new experimental solvation data (small molecules and amino acids) within the last 5 years? Thanks! From owner-chemistry@ccl.net Thu Aug 12 15:25:01 2010 From: "Oellien, F (Frank) frank.oellien%x%sp.intervet.com" To: CCL Subject: CCL: Final Call For Papers - German Conference on Chemoinformatics Message-Id: <-42518-100812120742-30652-aUjhZwSqjs+q/vte+kBStw+*+server.ccl.net> X-Original-From: "Oellien, F (Frank)" Content-class: urn:content-classes:message Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset="iso-8859-1" Date: Thu, 12 Aug 2010 18:07:27 +0200 MIME-Version: 1.0 Sent to CCL by: "Oellien, F (Frank)" [frank.oellien%a%sp.intervet.com] Final CALL FOR PAPERS 6th German Conference on Chemoinformatics Hotel 'Der Achtermann', Goslar, Germany 7 - 9 November 2010 Dear Colleagues, This is the final Call for Papers for the 6. German Conference on Chemoinformatics (http://www.gdch.de/gcc2010) to be held in Goslar, Germany, November 7 - 9, 2010. You can still submit abstracts until August 13, 2010!! Posters can still be submitted until August 31, 2010. Last minute posters can be submitted until October 9, 2010. We are inviting the submission of abstracts for talks and posters in the following plenary sessions: * Chemoinformatics and Drug Discovcery * Chemical Information, Patents, and Databases * Molecular Modelling * Computational Material Science and Nanotechnology In addition other highlights in the field of Computational Chemistry are also welcome. Invited Speakers this year are: * Colleen Fitzpatrick, Identifiers International, Huntington Beach, USA * Gerhard Klebe, University of Marburg, DE * Holger Gohlke, University of Dsseldorf, DE * Jrgen Gmehling, University of Oldenburg, DE * Hans Fraaije, University of Leiden, NL * Wolfang Guba, Roche, Basel, CH * Andrew R. Leach, GSK, Stevenage, UK Visit the conference website at www.gdch.de/gcc2010 for more information or access directly the Call-for-Paper PDF http://www.gdch.de/vas/tagungen/tg/einlad5412.pdf Frank Oellien GDCh CIC Chair Mit freundlichen Gren / With kind regards Dr. Frank Oellien BioChemInformatics Scientist Intervet Innovation GmbH Zur Propstei 55270 Schwabenheim, Germany E-Mail: frank.oellien[A]sp.intervet.com Phone: +49 (6130) 948 365 Fax: +49 (6130) 948 517 Home http://www.intervet.com A subsidiary of Merck & Co., Inc., Whitehouse Station, NJ, USA Sitz der Gesellschaft: Schwabenheim Amtsgericht Mainz, HRB 23 166 Geschftsfhrer: Dr. Peter Schmid From owner-chemistry@ccl.net Thu Aug 12 16:01:01 2010 From: "Jamin Krinsky jamink a berkeley.edu" To: CCL Subject: CCL:G: Basis set notation Message-Id: <-42519-100812155928-20744-ZVPwqScAmXlHoZYl9Mq1eg::server.ccl.net> X-Original-From: Jamin Krinsky Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 12 Aug 2010 12:59:12 -0700 MIME-Version: 1.0 Sent to CCL by: Jamin Krinsky [jamink*o*berkeley.edu] Hi John, Your answer is neither. The 6-31G(d',p' ) basis is just input format for the 6-31G(double-dagger) basis, see G. A. Petersson and M. A. Al-Laham, “A complete basis set model chemistry. II. Open-shell systems and the total energies of the first-row atoms,” J. Chem. Phys., 94 (1991) 6081-90. Gaussian's website states: 6-31G†: Gaussian 09 also includes the 6-31G† and 6-31G‡ basis sets of George Petersson and coworkers, defined as part of the Complete Basis Set methods [Petersson88, Petersson91]. These are accessed via the 6-31G(d') and 6-31G(d',p') keywords, to which single or double diffuse functions may also be added; f functions may also be added: e.g., 6-31G(d'f), and so on. So you could have 6-31++G(d',p'). Hope this helps. Regards, Jamin On Thu, Aug 12, 2010 at 7:32 AM, John McKelvey jmmckel- -gmail.com wrote: > > Sent to CCL by: John McKelvey [jmmckel|a|gmail.com] > I may be out of touch on this: > > I take the basis set notation 6-31G(d,p) to be the same as 6-31G**. > The question is whether or not the notation  6-31G(d',p' ) is accepted > as an alternative for 6-31++G**, or is (d',p') a notation I'm just out > of touch on? > > Thanks! > > John > -- > John McKelvey > 10819 Middleford Pl > Ft Wayne, IN 46818 > 260-489-2160 > jmmckel-#-gmail.com>      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.txt> > > -- Jamin L Krinsky, Ph.D. Molecular Graphics and Computation Facility 175 Tan Hall, University of California, Berkeley, CA 94720 jamink * berkeley.edu, 510-643-0616 http://glab.cchem.berkeley.edu From owner-chemistry@ccl.net Thu Aug 12 20:06:00 2010 From: "John McKelvey jmmckel%%gmail.com" To: CCL Subject: CCL:G: Basis set notation Message-Id: <-42520-100812181216-3930-EfSnuIES4i4+8Elo/U4gZg%%server.ccl.net> X-Original-From: John McKelvey Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 12 Aug 2010 18:12:07 -0400 MIME-Version: 1.0 Sent to CCL by: John McKelvey [jmmckel###gmail.com] Jamin... I agree... I was refereeing a paper and had not seen it before and some one at CCL pointed it out in the Gaussian manual.. Thanks.. John On Thu, Aug 12, 2010 at 3:59 PM, Jamin Krinsky jamink a berkeley.edu wrote: > > Sent to CCL by: Jamin Krinsky [jamink*o*berkeley.edu] > Hi John, > > Your answer is neither. The 6-31G(d',p' ) basis is just input format > for the 6-31G(double-dagger) basis, see G. A. Petersson and M. A. > Al-Laham, “A complete basis set model chemistry. II. Open-shell > systems and the total energies of the first-row atoms,” J. Chem. > Phys., 94 (1991) 6081-90. > > Gaussian's website states: > 6-31G†: Gaussian 09 also includes the 6-31G† and 6-31G‡ basis sets of > George Petersson and coworkers, defined as part of the Complete Basis > Set methods [Petersson88, Petersson91]. These are accessed via the > 6-31G(d') and 6-31G(d',p') keywords, to which single or double diffuse > functions may also be added; f functions may also be added: e.g., > 6-31G(d'f), and so on. > > So you could have 6-31++G(d',p'). Hope this helps. > > Regards, > Jamin > > On Thu, Aug 12, 2010 at 7:32 AM, John McKelvey jmmckel- -gmail.com > wrote: >> >> Sent to CCL by: John McKelvey [jmmckel|a|gmail.com] >> I may be out of touch on this: >> >> I take the basis set notation 6-31G(d,p) to be the same as 6-31G**. >> The question is whether or not the notation  6-31G(d',p' ) is accepted >> as an alternative for 6-31++G**, or is (d',p') a notation I'm just out >> of touch on? >> >> Thanks! >> >> John >> -- >> John McKelvey >> 10819 Middleford Pl >> Ft Wayne, IN 46818 >> 260-489-2160 >> jmmckel-#-gmail.com>      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.txt> >> >> > > > > -- > Jamin L Krinsky, Ph.D. > Molecular Graphics and Computation Facility > 175 Tan Hall, University of California, Berkeley, CA 94720 > jamink : berkeley.edu, 510-643-0616 > http://glab.cchem.berkeley.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.txt> > > -- John McKelvey 10819 Middleford Pl Ft Wayne, IN 46818 260-489-2160 jmmckel(_)gmail.com From owner-chemistry@ccl.net Thu Aug 12 20:41:02 2010 From: "Kadir Diri dirikadir!^!gmail.com" To: CCL Subject: CCL: "Shine a light" and "Laser" now in Russian Message-Id: <-42521-100812173041-4017-u2nYegaYdw6e5JTUWQsuKA,+,server.ccl.net> X-Original-From: Kadir Diri Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Thu, 12 Aug 2010 14:27:36 -0700 MIME-Version: 1.0 Sent to CCL by: Kadir Diri [dirikadir[*]gmail.com] Dear Colleagues, Upon request we now have our short educational movies "Shine a light" and "Laser" with Russian and Spanish subtitles: http://iopenshell.usc.edu/howto/education/ If you would like to contribute in spreading the joy of science to the non-expert masses all over the world by translating the script to other languages, we can send you the script. Enjoy! kadir --------------- Kadir Diri, PhD Research Scientist Department of Chemistry and iOpenShell Center SSC #401 University of Southern California Los Angeles, CA 90089-0482 -------------------------- Relativistic correction to Murphy's law: Whether things can go wrong or not, depends on your frame of reference.