From owner-chemistry@ccl.net Mon Jul 18 02:13:00 2011 From: "Rishi rish.iisc- -gmail.com" To: CCL Subject: CCL:G: Basis set Message-Id: <-45100-110718020258-15267-uxLo9BYL0a9Amrfiao5mQA[*]server.ccl.net> X-Original-From: Rishi Content-Type: multipart/alternative; boundary=bcaec520f191d5b53d04a851bfe9 Date: Mon, 18 Jul 2011 11:32:51 +0530 MIME-Version: 1.0 Sent to CCL by: Rishi [rish.iisc-.-gmail.com] --bcaec520f191d5b53d04a851bfe9 Content-Type: text/plain; charset=ISO-8859-1 Dear CCL users, I would like to carry out frequency calculation for a molecule (which contains Cl and S along with C,H and O atoms) in its lowest triplet state. I have attempted to calculate the frequencies(on optimized geom with same basis set) with DFT/B3LYP/6-311++g(d,p) using Gaussian 09 program suite but the calculated frequencies are not in good agreement with experimentally observed frequencies.I will appreciate if you can please suggest me the basis sets best suited for the molecules containing Chlorine and Sulphur. Thanks in advance Regards Rishi --bcaec520f191d5b53d04a851bfe9 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
Dear CCL users,
=A0
I would like to carry out frequency calculation for a molecule (which = contains Cl and S along with C,H and O atoms) in its lowest triplet state. = I have attempted to calculate the frequencies(on optimized geom with same b= asis set)=A0with DFT/B3LYP/6-311++g(d,p) using Gaussian=A009 program suite= =A0but the=A0calculated frequencies are not in good agreement with experime= ntally observed frequencies.I will appreciate =A0if you can please suggest = me the=A0basis=A0sets best=A0suited=A0for the molecules containing Chlorine= and Sulphur.
=A0
Thanks in advance
Regards
Rishi
--bcaec520f191d5b53d04a851bfe9-- From owner-chemistry@ccl.net Mon Jul 18 08:23:00 2011 From: "Adrian Stevens adrian.stevens() accelrys.com" To: CCL Subject: CCL: Announcing the release of Accelrys Discovery Studio 3.1 Message-Id: <-45101-110718071234-9130-mIkSbS9TapCqFKO7VatWDA]![server.ccl.net> X-Original-From: "Adrian Stevens" Date: Mon, 18 Jul 2011 07:12:30 -0400 Sent to CCL by: "Adrian Stevens" [adrian.stevens(a)accelrys.com] We are very pleased to announce the release of the latest version of Discovery Studio our integrated modeling and simulation solution for both small molecule and macromolecule-based research. DS3.1 includes many new features and enhancements including: * Science - A new scientific method to calculate the aggregation propensity of proteins has been added. This method in-licenses the patented spatial aggregation propensity methodology developed by the Massachusetts Institute of Technology in collaboration with a major pharmaceutical company. New enhancements to the interface have also been added to improve the ease of job deployment and analysis of results. - New X-ray crystallography functionality, HT-XPIPE, provides an automated pipeline for placement and refinement of protein-ligand complexes in high-throughput mode. - Enhancements to many of the Pharmacophore and Macromolecule protocols have been made. * Deployment - Full compatibility with Pipeline Pilot 8.5. * Collaboration - Discovery Studio 3.1 can now save 3D molecules directly to HTML and Microsoft PowerPoint slides. - Our free 3D plug-in, Discovery Studio ActiveX control, has been updated to support Discovery Studio 3.1. - New storyboard playback features have been added as well as the ability to export movies for ease of knowledge transfer. * Ecosystem - Updated support for GOLD (version 5.0.1) and NAMD (version 2.7). Webinar Series Extended: ------------------------ Accelrys will also be hosting a series of Discovery Studio live webinars which will include a Whats new in Discovery Studio 3.1 webinar on July 21st. Please visit our site to learn more and register: http://accelrys.com/events/webinars/discovery-studio-31/index.php. Downloading DS3.1: ------------------ DS3.1 is available for download at the Accelrys Customer Support Center: https://community.accelrys.com/community/support. Click the green Download Center button on the right side of the Support Center page to view software products available for download. Get our latest Free DS Visualizer and DS ActiveX Control! --------------------------------------------------------- Version 3.1 of our free DS Visualizer and DS ActiveX control can be downloaded for free at: http://accelrys.com/products/discovery-studio/visualization-download.php Best regards, Adrian Stevens Product Marketing Manager, Discovery Studio From owner-chemistry@ccl.net Mon Jul 18 13:13:01 2011 From: "Daniele Gianni daniele.gianni[]gmail.com" To: CCL Subject: CCL: WISC11 - EXTENDED DEADLINE, final CFP Message-Id: <-45102-110718125631-27951-nZvo4YgxuPBLulvEAcQ1hQ*o*server.ccl.net> X-Original-From: Daniele Gianni Content-Type: multipart/alternative; boundary=000e0cd598fedfab5304a85ae04d Date: Mon, 18 Jul 2011 18:56:20 +0200 MIME-Version: 1.0 Sent to CCL by: Daniele Gianni [daniele.gianni|-|gmail.com] --000e0cd598fedfab5304a85ae04d Content-Type: text/plain; charset=ISO-8859-1 IEEE e-Science 2011 Workshop on Interoperability in Scientific Computing ======================================================================== 5th December 2011, Stockholm, Sweden. http://www.cs.ox.ac.uk/david.johnson/wisc11/ **EXTENDED DEADLINE** **FULL PAPERS DUE: MONDAY 25th JULY 2011** The seventh IEEE e-Science conference, sponsored by the IEEE Computer Society's Technical Committee for Scalable Computing (TCSC), will be held in Stockholm, Sweden from 5th - 8th December 2011. The Workshop on Interoperability in Scientific Computing will be held on the morning of Monday 5th of December, and is co-located with the main conference. Approaches to modelling take many forms. The mathematical, computational and encapsulated components of models can be diverse in terms of complexity and scale, as well as in published implementation (mathematics, source code, and executable files). Many of these systems are attempting to solve real-world problems in isolation. However the long-term scientific interest is in allowing greater access to models and their data, and to enable simulations to be combined in order to address ever more complex issues. Markup languages, metadata specifications, and ontologies for different scientific domains have emerged as pathways to greater interoperability. Domain specific modelling languages allow for a declarative development process to be achieved. Metadata specifications enable coupling while ontologies allow cross platform integration of data. The goal of this workshop is to bring together researchers from across scientific disciplines whose computational models require interoperability. This may arise through interactions between different domains, systems being modelled, connecting model repositories, or coupling models themselves, for instance in multi-scale or hybrid simulations. The outcomes of this workshop will be to better understand the nature of multidisciplinary computational modelling and data handling. Moreover we hope to identify common abstractions and cross-cutting themes in future interoperability research applied to the broader domain of scientific computing. FINAL CALL FOR PAPERS We invite submissions for high-quality papers (up to 8 pages in length) within the context of scientific computing in any of the traditional sciences (physics, chemistry, biology), engineering, or scientific/mathematical modelling applied to the social sciences and humanities. Papers should address progress, results or positions in one or more of the following areas: * Use of metadata standards for annotating scientific models and data * Curating and publishing digital models and data to online repositories * Meta-modelling and markup languages for model description * Theoretical frameworks for combining disparate models, multi-scale models * Using standardised data formats in computational models * Domain-specific ontologies for the sciences It is expected that the proceedings of the e-Science 2011 workshops will be published by the IEEE Computer Society Press, USA, and will be made available online through the IEEE Digital Library. SUBMISSION PROCESS Authors are invited to submit papers with unpublished, original work of not more than 8 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines. Templates are available from here: http://www.ieee.org/web/publications/pubservices/confpub/AuthorTools/conferenceTemplates.html . Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers conforming to the above guidelines should be submitted through the EasyChair submission system here: https://www.easychair.org/account/signin.cgi?conf=wisc11 Note, papers should NOT be submitted to the main e-Science 2011 paper submission system, as they will not be directed to the workshop organisers. It is requested that at least one author of each accepted paper attend the conference and workshop. IMPORTANT DATES **EXTENDED DEADLINE** **FULL PAPERS DUE: MONDAY 25th JULY 2011** Notification of acceptance: 18th August 2011 Camera-ready: 16th September 2011 Workshop date: 5th December 2011 CHAIRS/ORGANISERS David Johnson, Steve McKeever, (University of Oxford, UK) PROGRAMME COMMITTEE David Nickerson (University of Auckland, New Zealand) Herbert Sauro (University of Washington, USA) Steve Harris (University of Oxford, UK) Jonathan Cooper (University of Oxford, UK) Rutger Vos (University of Reading, UK) Dagmar Waltemath (University of Rostock, Germany) Daniele Gianni (European Space Agency) Mike Stout (University of Nottingham, UK) --000e0cd598fedfab5304a85ae04d Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable
IEEE e-Science 2= 011 Workshop on Interoperability in Scientific Computing
=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=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=3D=3D
5th December 2011, Stockholm, Sweden.
http://www.cs.ox.ac.uk/david.johnson/wisc1= 1/
**EXTENDED DEADLINE**
**FULL PAPERS DUE: MONDAY 25th JULY 2011**

The seventh IEEE e-Science conference, sponsored by the IEEE Computer Socie= ty's Technical Committee for Scalable Computing (TCSC), will be held in Stockhol= m, Sweden from 5th - 8th December 2011. The Workshop on Interoperability in Scientific Computing will be held on the morning of Monday 5th of December, and is co-located with the main conference.

Approaches to modelling take many forms. The mathematical, computational and encapsulated components of models can be diverse in terms of complexity and scale, as well as in published implementation (mathematics, source code, and executable files). Many of these systems are attempting to solve real-world problems in isolation. However the long-term scientific interest is in allowing greater access to models and their data, and to enable simul= ations to be combined in order to address ever more complex issues. Markup languag= es, metadata specifications, and ontologies for different scientific domains have emerged as pathways to greater interoperability. Domain specific model= ling languages allow for a declarative development process to be achieved. Metad= ata specifications enable coupling while ontologies allow cross platform integr= ation of data.

The goal of this workshop is to bring together researchers from across scientific disciplines whose computational models require interoperability. This may arise through interactions between different domains, systems being modelled, connecting model repositories, or coupling models themselve= s, for instance in multi-scale or hybrid simulations. The outcomes of this workshop will be to better understand the nature of multidisciplinary compu= tational modelling and data handling. Moreover we hope to identify common abstractio= ns and cross-cutting themes in future interoperability research applied to the broader domain of scientific computing.

FINAL CALL FOR PAPERS

We invite submissions for high-quality papers (up to 8 pages in length) within the context of scientific computing in any of the traditional scienc= es (physics, chemistry, biology), engineering, or scientific/mathematical modelling applied to the social sciences and humanities. Papers should address progress, results or positions in one or more of the following areas:

* Use of metadata standards for annotating scientific models and data
* Curating and publishing digital models and data to online repositories * Meta-modelling and markup languages for model description
* Theoretical frameworks for combining disparate models, multi-scale models=
* Using standardised data formats in computational models
* Domain-specific ontologies for the sciences

It is expected that the proceedings of the e-Science 2011 workshops will be published by the IEEE Computer Society Press, USA, and will be made available online through the IEEE Digital Library.

SUBMISSION PROCESS

Authors are invited to submit papers with unpublished, original work of not more than 8 pages of double column text using single spaced 10 point size on 8.5 x 11 inch pages, as per IEEE 8.5 x 11 manuscript guidelines.
Templates are available from here:
http://www.ieee.org/web/publications/pubservices/confpub/AuthorTools= /conferenceTemplates.html.

Authors should submit a PDF or PostScript (level 2) file that will print on a PostScript printer. Papers conforming to the above guidelines should be submitted through the EasyChair submission system here:
https://www.easychair.org/ac= count/signin.cgi?conf=3Dwisc11

Note, papers should NOT be submitted to the main e-Science 2011 paper submi= ssion system, as they will not be directed to the workshop organisers.

It is requested that at least one author of each accepted paper attend the conference and workshop.

IMPORTANT DATES
**EXTENDED DEADLINE**
**FULL PAPERS DUE: MONDAY 25th JULY 2011**
Notification of acceptance: 18th August 2011
Camera-ready: 16th September 2011
Workshop date: 5th December 2011

CHAIRS/ORGANISERS

David Johnson, Steve McKeever, (University of Oxford, UK)

PROGRAMME COMMITTEE

David Nickerson (University of Auckland, New Zealand)
Herbert Sauro (University of Washington, USA)
Steve Harris (University of Oxford, UK)
Jonathan Cooper (University of Oxford, UK)
Rutger Vos (University of Reading, UK)
Dagmar Waltemath (University of Rostock, Germany)
Daniele Gianni (European Space Agency)
Mike Stout (University of Nottingham, UK)





--000e0cd598fedfab5304a85ae04d-- From owner-chemistry@ccl.net Mon Jul 18 14:12:00 2011 From: "S M mandegar_saman%%yahoo.com" To: CCL Subject: CCL:G: G09: Ground to excited state transition electric dipole moments Message-Id: <-45103-110718141013-20075-T+Nwv5iGwiCuGP7BH5+Fkg,server.ccl.net> X-Original-From: "S M" Date: Mon, 18 Jul 2011 14:10:09 -0400 Sent to CCL by: "S M" [mandegar_saman*yahoo.com] Dear All, The standard Gaussian09 output gives the components of the transition electric dipoles with few decimal digits (4) which can lead to sensible accuracy problems for the derivatives. I just modified the related link (putil.F) to print put more decimal digits in the source code and recompiled Gaussian again. In fact changed F11.4 to F4.11 in the format (to print 11 dcimal) but the output sounds wired as folling. Is there any body have experience with this issue? Any help is greatly appreciated. Excited states from singles matrix: *********************************************************************** Ground to excited state transition electric dipole moments (Au): state X Y Z Dip. S. Osc. 1 **** **** **** **** **** 2 **** **** **** **** **** 3 **** **** **** **** **** Ground to excited state transition velocity dipole moments (Au): state X Y Z Dip. S. Osc. 1 **** **** **** **** **** 2 **** **** **** **** **** 3 **** **** **** **** **** Thanks®ards, Saman From owner-chemistry@ccl.net Mon Jul 18 22:59:01 2011 From: "Mehboob Alam mehboob.cu[]gmail.com" To: CCL Subject: CCL:G: G09: Ground to excited state transition electric dipole moments Message-Id: <-45104-110718225647-7573-/jnGhlt/9Yox/Zi1nxF3Mw..server.ccl.net> X-Original-From: Mehboob Alam Content-Type: multipart/alternative; boundary=0015177415b4d95f8704a8634381 Date: Tue, 19 Jul 2011 08:26:40 +0530 MIME-Version: 1.0 Sent to CCL by: Mehboob Alam [mehboob.cu%gmail.com] --0015177415b4d95f8704a8634381 Content-Type: text/plain; charset=ISO-8859-1 Dear Saman, This is a space problem..I mean to say when you are declaring F4.11 it means that you allowing only 4 space and saying to print 11 digits after decimal... this is not valid...according to my opinion if you can declare F25.11 then you will get the proper result...in general in Fx.y format x should be larger than y. Hope it will help. With best regards Mehboob On Mon, Jul 18, 2011 at 11:40 PM, S M mandegar_saman%%yahoo.com < owner-chemistry-#-ccl.net> wrote: > > Sent to CCL by: "S M" [mandegar_saman*yahoo.com] > Dear All, > The standard Gaussian09 output gives the components of the > transition electric dipoles with few decimal digits (4) which can lead to > sensible accuracy problems for the derivatives. I just modified the related > link (putil.F) to print put more decimal digits in the source code and > recompiled Gaussian again. In fact changed F11.4 to F4.11 in the format (to > print 11 dcimal) but the output sounds wired as folling. Is there any body > have experience with this issue? Any help is greatly appreciated. > > > > Excited states from singles matrix: > *********************************************************************** > > Ground to excited state transition electric dipole moments (Au): > state X Y Z Dip. S. Osc. > 1 **** **** **** **** **** > 2 **** **** **** **** **** > 3 **** **** **** **** **** > Ground to excited state transition velocity dipole moments (Au): > state X Y Z Dip. S. Osc. > 1 **** **** **** **** **** > 2 **** **** **** **** **** > 3 **** **** **** **** **** > > Thanks®ards, > Saman> > > --0015177415b4d95f8704a8634381 Content-Type: text/html; charset=ISO-8859-1 Content-Transfer-Encoding: quoted-printable Dear Saman,

This is a space problem..I mean to say when = you are declaring F4.11 it means that you allowing only 4 space and saying = to print 11 digits after decimal... this is not valid...according to my opi= nion if you can declare F25.11 then you will get the proper result...in gen= eral in Fx.y format x should be larger than y. Hope it will help.

With best regards
Mehboob

On Mon, Jul 18, 2011 at 11:40 PM, S M mandegar_saman%= %yahoo.com <owner-chemistry-#-ccl.net> = wrote:

Sent to CCL by: "S =A0M" [mandegar_saman*yahoo.com]
Dear All,
The standard Gaussian09 output gives the components of the
transition electric dipoles with few decimal digits (4) which can lead to sensible accuracy problems for the derivatives. I just modified the related=
link (putil.F) to print put more decimal digits in the source code and
recompiled Gaussian again. In fact changed F11.4 to F4.11 in the format (to=
print 11 dcimal) but the output sounds wired as folling. Is there any body<= br> have experience =A0with this issue? Any help is greatly appreciated.



Excited states from <AA,BB:AA,BB> singles matrix:
=A0***********************************************************************<= br>
=A0Ground to excited state transition electric dipole moments (Au):
=A0 =A0 =A0 state =A0 =A0 =A0 =A0 =A0X =A0 =A0 =A0 =A0 =A0 Y =A0 =A0 =A0 = =A0 =A0 Z =A0 =A0 =A0 =A0Dip. S. =A0 =A0 =A0Osc.
=A0 =A0 =A0 =A0 1 =A0 =A0**** **** **** **** ****
=A0 =A0 =A0 =A0 2 =A0 =A0**** **** **** **** ****
=A0 =A0 =A0 =A0 3 =A0 =A0**** **** **** **** ****
=A0Ground to excited state transition velocity dipole moments (Au):
=A0 =A0 =A0 state =A0 =A0 =A0 =A0 =A0X =A0 =A0 =A0 =A0 =A0 Y =A0 =A0 =A0 = =A0 =A0 Z =A0 =A0 =A0 =A0Dip. S. =A0 =A0 =A0Osc.
=A0 =A0 =A0 =A0 1 =A0 =A0**** **** **** **** ****
=A0 =A0 =A0 =A0 2 =A0 =A0**** **** **** **** ****
=A0 =A0 =A0 =A0 3 =A0 =A0**** **** **** **** ****

Thanks&regards,
Saman



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