From owner-chemistry@ccl.net Mon Nov 9 02:54:00 2009 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre{}univ-provence.fr" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40648-091109025158-31395-8MtSGoS+eigd+zJ5jcvGYQ#server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 09 Nov 2009 08:51:35 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre:+:univ-provence.fr] Suggestions: SAPT? Morokuma's energy decomposition? NBO/NRT? There are more than a couple of schemes to separate the interaction energy in several components. If you are interested into the electrostatic part only, fit some charges or multipoles to one ion and use them to polarize the other one wavefunction. And repeat this scheme to fit multipoles of the second ion that will be used to polarize the first ion wfn. And repeat again until you reach convergence. NF Green Power powergreen*_*gmail.com a écrit : > Dear Mahmoud, Morad and Nicolas, > > First, thank you for your comments. Maybe I should describe more > question more clearly. In a VB model, a diatomic bond can be simply > described by spin paring, A-B, A(-)-B(+) and A(+)-B(-1). In VB picture, > we can easily learn the relative weight of the respective VB structures. > In Hubbard model description, the relative weight of the ionic > structures depends on the onsite Coulomb repulsion, intersite repulsion > and the polarization energy between the cation and the anion. With the > two layer A(-1)...B(+1) ONIOM model in my previous email, I hope to > guesstimate the polrization energy between the two ions. Thus, the > charges on A(-1) should be embedded in the B(+) Hamiltonion, and the > charges on (B+) should be embedded in the A(-1) Hamiltonian. But I am > not sure if this is meaningful and I don't know how to do that. > > Best regards > > Roy > > 2009/11/8 Nicolas Ferré nicolas.ferre|a|univ-provence.fr > > > > > Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= > [nicolas.ferre.:.univ-provence.fr ] > Sorry, but I don't understand the aim of this discussion. The Oniom > method is a substractive scheme: > > E=E(A,high level)-E(A,low level)+E(A+B,low level) > > In the present case: high level=low level => E=E(A+B)!!! Basically > it is a standard non-Oniom calculation. > > Maybe I miss something, but it seems your calculation is not really > meaningfull ... > > NF > > Morad El-Hendawy m80elhendawy(~)yahoo.com a écrit : > > Hey Roy, > It is easy to model QM/QM by the same method i.e. B3LYP and the > same basis set e.g. 6-31+G** . You can carry out this using > Gaussview. I did a simple example to check that, CH3+NH- it gave > a normal termination and it is right. Take care, you have to > determine the two centeral atoms in both parts, here C+ and N-. > As you know there is no pure ionic bond, for example the bonding > between C+ and N- has a partial covalent charecter so you have > to set a suitable distance between two center, here for example > 1.5 Ang. Please after you succeed in your calculation, let us > know how to overcome difficulties faced you. > Good luck, > > **************************************************************************************************** > *Morad 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 until it come. * > ********************************************************************************************************************* > ** > > --- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim > m.ibrahim1982:-:yahoo.com > />/* wrote: > > > From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com > > > > Subject: CCL: ONIOM calculations > To: "El-Hendawy, Morad Metwally " > > Date: Sunday, November 8, 2009, 3:41 PM > > Dear Roy > Let's declear some points here: > Is there a difference between treating your system as two > QM-B3LYP > layers and as one QM-B3LYP layer? in other words, what is the > difference between QM(B3LYP):QM(B3LYP) and QM(B3LYP) for all the > system. As I believe, in general speaking, they are the same, > but in > your case, you specify that part A has a charge of a unit > value and > part B has a unit value of charge, and during optimization, each > part's charge will change with keeping its overall charge unity. > i.e. say, A's charge -1 and B's charge +1, so after optimization, > A's charge will be -1 and B's will be +1, but in case of > using only > one QM(B3LYP) for the whole system, in this case, > optimization will > lead to an overall charge of 0 without any limitation on > keeping A's > charge equals to -1 and B's charge equal to +1. > Roy, is it chemically right to make a limitation on the charge of > one part of your system? charge is a big challeng. Take care!!! > Roy, I don't know exactly what are you going to do, but have > a look > on Charge Keyword and R.E.D. program, they may open new thinking > ways for you. > Sincerely; > M. Ibrahim > Mahmoud A. A. Ibrahim > Current Address > School of Chemistry, University of Manchester, > Oxford Road, Manchester, M13 9PL, United Kingdom. > > Home Address > Chemistry Department, Faculty of Science, > Minia University, > Minia 61519,Egypt. > > Contact Information > Email: m.ibrahim#,#compchem.net > Email: m.ibrahim1982#,#yahoo.com > Website: www.compchem.net > Fax No.: +20862342601 > > > --- On *Sun, 11/8/09, Green Power powergreen^-^gmail.com > > />/* wrote: > > > From: Green Power powergreen^-^gmail.com > > > Subject: CCL: ONIOM calculations > To: "Ibrahim, Mahmoud A. A. " > > Date: Sunday, November 8, 2009, 9:15 AM > > Dear All, > > Can I have a question about two layer ONIOM calculations. > For a > A(-)...B(+) system, I want to learn how the negtive > charged A(-) > is polarized by the positive charged B(+). I would like > to know > whether it is meaningfull to use the same theory levels, say > B3LYP, for the two layers. This seems to me like a QM:QM > model, > instead of QM:MM which seems more meaningfull to me, Your > valuable comments and suggestions are highly appriciated. > > Roy > > > > > > -- > Nicolas Ferre' > Laboratoire Chimie Provence > Universite' de Provence - France > Tel: +33 491282733 > http://sites.univ-provence.fr/lcp-ct> > > > E-mail to subscribers: CHEMISTRY*o*ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST*o*ccl.net > or useConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > -- Nicolas Ferre' Laboratoire Chimie Provence Universite' de Provence - France Tel: +33 491282733 http://sites.univ-provence.fr/lcp-ct From owner-chemistry@ccl.net Mon Nov 9 03:29:00 2009 From: "=?ISO-8859-1?Q?Nicolas_Ferr=E9?= nicolas.ferre-x-univ-provence.fr" To: CCL Subject: CCL: ONIOM calculations Message-Id: <-40649-091109025942-1792-TSV2hu6xlMayg7/XHIT1vQ{}server.ccl.net> X-Original-From: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=ISO-8859-1; format=flowed Date: Mon, 09 Nov 2009 08:59:27 +0100 MIME-Version: 1.0 Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= [nicolas.ferre]^[univ-provence.fr] Thank you for this obvious answer that would have enjoyed La Palice. NF Mahmoud A. A. Ibrahim m.ibrahim1982-.-yahoo.com a écrit : > Dear Nicolas Ferré > You are absolutely right, Two QM/QM with same bases set job is the same > as one QM job, but this is right in regarding to the Energy. But, > regarding to charge, there is a difference related to making restrains > on the overall charge of separated layers and the whole system. > Do one test job, and compare the charges of the atoms and layers. > Sincerely; > M. Ibrahim > > > Mahmoud A. A. Ibrahim > Current Address > School of Chemistry, University of Manchester, > Oxford Road, Manchester, M13 9PL, United Kingdom. > > Home Address > Chemistry Department, Faculty of Science, > Minia University, > Minia 61519,Egypt. > > Contact Information > Email: m.ibrahim(!)compchem.net > Email: m.ibrahim1982(!)yahoo.com > Website: www.compchem.net > Fax No.: +20862342601 > > > --- On *Sun, 11/8/09, Nicolas Ferré nicolas.ferre|a|univ-provence.fr > //* wrote: > > > From: Nicolas Ferré nicolas.ferre|a|univ-provence.fr > > Subject: CCL: ONIOM calculations > To: "Ibrahim, Mahmoud A. A. " > Date: Sunday, November 8, 2009, 6:24 PM > > > Sent to CCL by: =?ISO-8859-1?Q?Nicolas_Ferr=E9?= > [nicolas.ferre.:.univ-provence.fr] > Sorry, but I don't understand the aim of this discussion. The Oniom > method is a substractive scheme: > > E=E(A,high level)-E(A,low level)+E(A+B,low level) > > In the present case: high level=low level => E=E(A+B)!!! Basically > it is a standard non-Oniom calculation. > > Maybe I miss something, but it seems your calculation is not really > meaningfull ... > > NF > > Morad El-Hendawy m80elhendawy(~)yahoo.com a écrit : > > Hey Roy, > > It is easy to model QM/QM by the same method i.e. B3LYP and the > same basis set e.g. 6-31+G** . You can carry out this using > Gaussview. I did a simple example to check that, CH3+NH- it gave a > normal termination and it is right. Take care, you have to determine > the two centeral atoms in both parts, here C+ and N-. As you know > there is no pure ionic bond, for example the bonding between C+ and > N- has a partial covalent charecter so you have to set a suitable > distance between two center, here for example 1.5 Ang. Please after > you succeed in your calculation, let us know how to overcome > difficulties faced you. > > Good luck, > > > > > **************************************************************************************************** > > *Morad 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 until it come. * > > > ********************************************************************************************************************* > > ** > > > > --- On *Sun, 11/8/09, Mahmoud A. A. Ibrahim > m.ibrahim1982:-:yahoo.com //* wrote: > > > > > > From: Mahmoud A. A. Ibrahim m.ibrahim1982:-:yahoo.com > > > > Subject: CCL: ONIOM calculations > > To: "El-Hendawy, Morad Metwally " > > Date: Sunday, November 8, 2009, 3:41 PM > > > > Dear Roy > > Let's declear some points here: > > Is there a difference between treating your system as two > QM-B3LYP > > layers and as one QM-B3LYP layer? in other words, what is the > > difference between QM(B3LYP):QM(B3LYP) and QM(B3LYP) for all the > > system. As I believe, in general speaking, they are the same, > but in > > your case, you specify that part A has a charge of a unit > value and > > part B has a unit value of charge, and during optimization, each > > part's charge will change with keeping its overall charge unity. > > i.e. say, A's charge -1 and B's charge +1, so after optimization, > > A's charge will be -1 and B's will be +1, but in case of > using only > > one QM(B3LYP) for the whole system, in this case, > optimization will > > lead to an overall charge of 0 without any limitation on > keeping A's > > charge equals to -1 and B's charge equal to +1. > > Roy, is it chemically right to make a limitation on the charge of > > one part of your system? charge is a big challeng. Take care!!! > > Roy, I don't know exactly what are you going to do, but have > a look > > on Charge Keyword and R.E.D. program, they may open new thinking > > ways for you. > > Sincerely; > > M. Ibrahim > > Mahmoud A. A. Ibrahim > > Current Address > > School of Chemistry, University of Manchester, > > Oxford Road, Manchester, M13 9PL, United Kingdom. > > > > Home Address > > Chemistry Department, Faculty of Science, > > Minia University, > > Minia 61519,Egypt. > > > > Contact Information > > Email: m.ibrahim#,#compchem.net > > Email: m.ibrahim1982#,#yahoo.com > > Website: www.compchem.net > > Fax No.: +20862342601 > > > > > > --- On *Sun, 11/8/09, Green Power powergreen^-^gmail.com > > //* wrote: > > > > > > From: Green Power powergreen^-^gmail.com > > > Subject: CCL: ONIOM calculations > > To: "Ibrahim, Mahmoud A. A. " > > Date: Sunday, November 8, 2009, 9:15 AM > > > > Dear All, > > > > Can I have a question about two layer ONIOM calculations. > For a > > A(-)...B(+) system, I want to learn how the negtive > charged A(-) > > is polarized by the positive charged B(+). I would like > to know > > whether it is meaningfull to use the same theory levels, say > > B3LYP, for the two layers. This seems to me like a QM:QM > model, > > instead of QM:MM which seems more meaningfull to me, Your > > valuable comments and suggestions are highly appriciated. > > > > Roy > > > > > > > > > -- Nicolas Ferre' > Laboratoire Chimie Provence > Universite' de Provence - France > Tel: +33 491282733 > http://sites.univ-provence.fr/lcp-ct> the strange characters on the top line to the (!) sign. You can also> > E-mail to subscribers: CHEMISTRY(!)ccl.net > or use:> > E-mail to administrators: CHEMISTRY-REQUEST(!)ccl.net > or usehttp://www.ccl.net/chemistry/sub_unsub.shtmlConferences: > http://server.ccl.net/chemistry/announcements/conferences/> > > From owner-chemistry@ccl.net Mon Nov 9 06:52:01 2009 From: "Val Gillet v.gillet[*]sheffield.ac.uk" To: CCL Subject: CCL: Sheffield Chemoinformatics Conference 2010: Call for Papers Message-Id: <-40650-091109064859-12671-ULOBJtRtTCXmwBGFO6yQRQ|*|server.ccl.net> X-Original-From: "Val Gillet" Date: Mon, 9 Nov 2009 06:48:55 -0500 Sent to CCL by: "Val Gillet" [v.gillet]*[sheffield.ac.uk] Fifth Joint Sheffield Conference on Chemoinformatics: Call for Papers University of Sheffield 13th-15th July 2010 http://cisrg.shef.ac.uk/shef2010 organised on behalf of The Chemical Structure Association Trust and the Molecular Graphics and Modelling Society. The conference will be held in The Octagon Centre and the Edge Hall of Residence, University of Sheffield, UK. Offers of papers are welcomed on new developments in all aspects of chemoinformatics.Possible topics include (but are not limited to): * Virtual Screening including: docking and pharmacophore analysis, similarity and clustering methods; machine learning * Computational Methods for Lead Identification and Optimisation including: modelling and structure-activity methods; structure-based design; ADMET prediction; de novo design * High-Throughput Screening, including: assay quality control; design of screening collections; systems based design * New Algorithms and Technologies including: data mining; distributed processing; cloud computing; data handling and visualisation * Emerging applications including: SAR transfer between series; assessing the druggability of targets; the semantic web; large scale predictive modelling * Case Histories, incorporating practical experience of any of the above The programme will have space for ca. two dozen oral presentations, and there will also be extensive opportunities for poster presentations. Authors wishing to submit a paper should complete the template that will be provided in the near future at: http://cisrg.shef.ac.uk/shef2010 stating whether they wish to be considered for oral or for poster presentation. Abstracts should be 250-500 words in length. The deadline for abstract submission is 31st January 2010. Submissions will be selected for oral or poster presentation by the Programme Committee, with notification of acceptance by 28th February 2010. In selecting papers for oral presentation, the Committee will seek to achieve a balance between the various areas of the subject and between new methodologies and successful applications of existing techniques. Further details of the conference, including registration information and opportunities for sponsorship and participation in the conference exhibition will be posted at the conference website http://cisrg.shef.ac.uk/shef2010 or can be obtained from cheminf2010++sheffield.ac.uk From owner-chemistry@ccl.net Mon Nov 9 11:20:00 2009 From: "John Edward contact.||.promoteresearch.org" To: CCL Subject: CCL: BCBGC-10 Call for papers Message-Id: <-40651-091108190127-5310-EBDBcjz64yYBfQ+sGABRNA||server.ccl.net> X-Original-From: "John Edward" Date: Sun, 8 Nov 2009 19:01:22 -0500 Sent to CCL by: "John Edward" [contact!^!promoteresearch.org] BCBGC-10 Call for papers The 2010 International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) (website: http://www.PromoteResearch.org) will be held during 12-14 of July 2010 in Orlando, FL, USA. BCBGC is an important event in the areas of bioinformatics, computational biology, genomics and chemoinformatics and focuses on all areas related to the conference. The conference will be held at the same time and location where several other major international conferences will be taking place. The conference will be held as part of 2010 multi-conference (MULTICONF-10). MULTICONF-10 will be held during July 12-14, 2010 in Orlando, Florida, USA. The primary goal of MULTICONF is to promote research and developmental activities in computer science, information technology, control engineering, and related fields. Another goal is to promote the dissemination of research to a multidisciplinary audience and to facilitate communication among researchers, developers, practitioners in different fields. The following conferences are planned to be organized as part of MULTICONF-10. International Conference on Artificial Intelligence and Pattern Recognition (AIPR-10) International Conference on Automation, Robotics and Control Systems (ARCS-10) International Conference on Bioinformatics, Computational Biology, Genomics and Chemoinformatics (BCBGC-10) International Conference on Computer Networks (CN-10) International Conference on Enterprise Information Systems and Web Technologies (EISWT-10) International Conference on High Performance Computing Systems (HPCS-10) International Conference on Information Security and Privacy (ISP-10) International Conference on Image and Video Processing and Computer Vision (IVPCV-10) International Conference on Software Engineering Theory and Practice (SETP-10) International Conference on Theoretical and Mathematical Foundations of Computer Science (TMFCS-10) We invite draft paper submissions. Please see the website http://www.PromoteResearch.org for more details. Sincerely John Edward Publicity committee From owner-chemistry@ccl.net Mon Nov 9 19:10:01 2009 From: "Joy Ku joyku]*[stanford.edu" To: CCL Subject: CCL: New release of OpenMM and OpenMM-accelerated GROMACS for GPUs Message-Id: <-40652-091109185918-27304-ZCu3eBnH8A98O2NDtLFodA+*+server.ccl.net> X-Original-From: "Joy Ku" Date: Mon, 9 Nov 2009 18:59:15 -0500 Sent to CCL by: "Joy Ku" [joyku[A]stanford.edu] The 1.0 Beta version of OpenMM has just been released. OpenMM is a freely downloadable, high performance, extensible library that allows molecular dynamics (MD) simulations to run on high performance computer architectures, such as graphics processing units (GPUs). It currently supports NVIDIA GPUs and provides preliminary support for the new cross-platform, parallel programming standard OpenCL, which will enable it to be used on ATI GPUs. The new release includes support for Particle Mesh Ewald and custom non-bonded interactions. In conjunction with this release, a new version of the code needed for accelerating the GROMACS molecular dynamics software using OpenMM is also available. OpenMM is a collaborative project between Vijay Pandes lab at Stanford University and Simbios, the National Center for Physics-based Simulation of Biological Structures at Stanford, which is supported by the National Institutes of Health. For more information on OpenMM, go to http://simtk.org/home/openmm.