From owner-chemistry@ccl.net Thu Nov 6 04:29:01 2014 From: "Mariusz Radon mariusz.radon(-)gmail.com" To: CCL Subject: CCL: UV-vis in ORCA Message-Id: <-50704-141106035118-10242-NjblqZL+k7zjQU36+ZF/sA*|*server.ccl.net> X-Original-From: Mariusz Radon Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=UTF-8 Date: Thu, 06 Nov 2014 09:44:11 +0100 MIME-Version: 1.0 Sent to CCL by: Mariusz Radon [mariusz.radon%%gmail.com] On 11/05/2014 11:01 AM, Henrique Junior henriquecsj:+:gmail.com wrote: > Hi, my name is Henrique and I am an undergraduate student in Chemistry > doing some theoretical research about Fe(II) in water as a requirement > to finish my graduation. > > I’ve been using ORCA to perform some calculations and to generate UV-vis > spectra of [Fe(OH2)6]2+ and [Fe(OH2)6]3+. > > The result for [Fe(OH2)6]2+ is pretty much what I was expecting, but for > [Fe(OH2)6]3+ it seems a little weird to me: > > Since the d5 Iron(III) have only spin forbidden transitions, I wasn’t > expecting it to have more intense Abs than iron(II) (see attachment). > Dear Henrique: You are correct that for high-spin iron(III) complex all the d-d transitions are spin-forbidden, therefore will have exactly zero intensity (unless you include spin-orbit coupling in your calculations). Moreover, for centro-symmetric complexes, such as [Fe(H2O)6](3+), all the d-d transtions are also parity-forbidden (as gerade-to-gerade transitions they are forbidden by the Laporte rule). Hence, even if d-d the transitions were spin-allowed, the intensities calculated in TD-DFT will be zero for the ideal, centro-symmetric structure. To calculate intensities of such parity-forbidden transition correctly, you will need to consider coupling with molecular vibrations (of ungerade symmetry), which is far from being trivial. Therefore, I am afraid you cannot obtain correct intensities for such parity-forbidden d-d transitions > from single-point TD-DFT calculations. The intense absorption you have for Fe(III) at ca. 400 nm is almost certainly due to ligand-to-metal charge transfer transitions. Such transitions can be spin- and parity- allowed, thereby they will generate intense absorption bands. Best regards, Mariusz Radoń -- Dr Mariusz Radon, Ph.D. Coordination Chemistry Group Faculty of Chemistry Jagiellonian University ul. Ingardena 3, 30-060 Krakow, Poland http://www2.chemia.uj.edu.pl/~mradon From owner-chemistry@ccl.net Thu Nov 6 06:00:00 2014 From: "Georg Lefkidis lefkidis(a)physik.uni-kl.de" To: CCL Subject: CCL: McChurchie-Davidson algorithm Message-Id: <-50705-141106055758-31311-gccLWVHxExQ0RrOUIeEBBw^_^server.ccl.net> X-Original-From: "Georg Lefkidis" Content-Language: de Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset="us-ascii" Date: Thu, 6 Nov 2014 11:58:19 +0100 MIME-Version: 1.0 Sent to CCL by: "Georg Lefkidis" [lefkidis_-_physik.uni-kl.de] Dear all, I am trying to create a Fortran 90 program that calculates 2-electron integrals (Coulomb + exchange + derivatives) using the McMurchie-Davidson scheme. I have worked out all the recursion formulas for Coulomb, derivatives etc. and they work fine in isolation. However, it turns out to be a formidable task to bring it to a form that finishes calculation within an acceptable time frame.... I understand that pretabulation should be performed as much as possible, but obviously I am not carrying it out to the extent needed. Can someone point me to some relative literature? What I need is not the mathematical formulation of the MD scheme (this I know) but help with its algorithmic implementation. Using an already compiled program as a black-box is not really an option, since I wish to modify and calculate additional two-electron-additional integrals (multiple derivatives etc). Besides I really want to understand how it works. Best regards George From owner-chemistry@ccl.net Thu Nov 6 07:20:01 2014 From: "Partha Sengupta anapspsmo ~ gmail.com" To: CCL Subject: CCL: Gaussian calculation for 3 dimensional crystal Message-Id: <-50706-141106065453-25591-er21KhxPt4ByONE83aa9bw-x-server.ccl.net> X-Original-From: Partha Sengupta Content-Type: multipart/alternative; boundary=001a11c238aef71b6d05072f5c32 Date: Thu, 6 Nov 2014 17:24:48 +0530 MIME-Version: 1.0 Sent to CCL by: Partha Sengupta [anapspsmo]^[gmail.com] --001a11c238aef71b6d05072f5c32 Content-Type: text/plain; charset=UTF-8 Friends, How can I calculate the properties of a crystal in three dimension ? PSSengupta -- Dr. Partha Sarathi Sengupta Associate Professor Vivekananda Mahavidyalaya, Burdwan --001a11c238aef71b6d05072f5c32 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable
Friends, How can I calculate the properties of a crystal i= n three dimension ?
PSSengupta

--
<= div class=3D"gmail_signature">Dr. Partha Sarathi Sengupta
Associate Prof= essor
Vivekananda Mahavidyalaya, Burdwan
--001a11c238aef71b6d05072f5c32-- From owner-chemistry@ccl.net Thu Nov 6 08:44:00 2014 From: "Marcel Swart marcel.swart[A]icrea.cat" To: CCL Subject: CCL: Results of DFT14poll Message-Id: <-50707-141106084219-13300-IGWnYIicdIUBLUY+548zzA() server.ccl.net> X-Original-From: Marcel Swart Content-Transfer-Encoding: 8bit Content-Type: text/plain; charset=us-ascii Date: Thu, 6 Nov 2014 14:42:12 +0100 Mime-Version: 1.0 (Mac OS X Mail 8.0 \(1990.1\)) Sent to CCL by: Marcel Swart [marcel.swart^icrea.cat] Finally we have been able to present the results of the DFT popularity poll. This year is a special year, because it is the 5th edition of the poll. Because of this special year, we have added to the news-item some additional sections where we give a historical account, describe anecdotes and report on the current and future status of the poll. We had also asked several experienced researchers in the field whether they were in favor or against the poll. Their responses can be read both in the news-item and at the Nature Chemistry blog: since it is a special year for the DFT poll, the team of Nature Chemistry was so kind to let us write a guest piece on their blog. http://www.marcelswart.eu/dft-poll http://blogs.nature.com/thescepticalchymist (or to go directly to the post: http://blogs.nature.com/thescepticalchymist/2014/11/five-years-of-polling-the-computational-chemistry-community.html) Marcel Swart Matthias Bickelhaupt Miquel Duran From owner-chemistry@ccl.net Thu Nov 6 11:51:01 2014 From: "David Soriano d.soriano|,|acellera.com" To: CCL Subject: CCL: Maxwell GPU review for MD simulations - new hardware - and more... Message-Id: <-50708-141106110259-10942-qf3V0voBYX10vW5NkwaiCA]*[server.ccl.net> X-Original-From: "David Soriano" Date: Thu, 6 Nov 2014 11:02:58 -0500 Sent to CCL by: "David Soriano" [d.soriano#,#acellera.com] Hi all, A while ago we launched a blog in our website. The following lines direct you to it and to other changes we've made to our line of products and services. Products: Metrocubo hardware now shipping with latest Maxwell GPUs (280ns/day DHFR 1GPU) For more info: Metrocubo workstation http://www.acellera.com/products/gpu-hardware-molecular-dynamics-metrocubo/ Metrocubo G server http://www.acellera.com/products/gpu-cluster-molecular-dynamics-cadd-metrocubo-g/ Also, ask for our end of the year offers. Blog: Review of Maxwell GPUs in all atom MD (by Matt Harvey. Acellera CTO) http://www.acellera.com/maxwell-gtx980-molecular-dynamics-gm204-gpu/ Nat. Comm. article highlight: Kinetic modulation of an IDP by phosphorylation (by Santi Esteban, author) http://www.acellera.com/phosphorylation-regulation-idp-kinetics-molecular- dynamics/ Services/projects: Data service significant price drop. Ask for more info. Projects: We are now using adaptive sampling methodology. Our throughput has increased. Be sure to check our webpage of the next few weeks as we are just about to introduce an exciting new product. First users will get a significantly discounted introductory rate. Best regards, The Acellera Team From owner-chemistry@ccl.net Thu Nov 6 13:31:01 2014 From: "Elaine Meng meng[]cgl.ucsf.edu" To: CCL Subject: CCL: new Chimera release (1.10) Message-Id: <-50709-141106124234-10727-IAgnd2A2Q0yBfuQHGnanKQ^server.ccl.net> X-Original-From: "Elaine Meng" Date: Thu, 6 Nov 2014 12:42:33 -0500 Sent to CCL by: "Elaine Meng" [meng{=}cgl.ucsf.edu] Hello everybody, A new production release of UCSF Chimera (version 1.10) is available: http://www.rbvi.ucsf.edu/chimera/download.html Download is free for noncommercial use. Platforms: Windows, Mac OS X (including Yosemite), Linux. This will be the last release to support OS X 10.6 and 10.7. New since version 1.9: Protein contact maps color-coded by distance, PDB biounit and CATH domain web fetch, plotting all-atom and backbone RMSDs along sequence alignments (previously only alpha-carbon RMSDs), update to AmberTools 14, "vop scale" density map normalization, Modeller dialog allows specifying distance restraints, further implementation of the MultiDomain Assembler homology-modeling pipeline. More details are given below; see release notes for the full list: http://www.rbvi.ucsf.edu/chimera/docs/relnotes/1.10.html I/O, Display: * new web fetch options: PDB biounit, CATH domain * improved New Molecules preferences (initial structure display) * protein SSE (secondary structure element) inserted into up/down-arrow selection cascade * shortcuts rn, rp, ri to shift the selection to the next, previous, and intervening residues in a chain * "rainbow" command can assign a unique color to each SSE * green-magenta (trioscopic) stereo mode * new input format: COLLADA (.dae) Structure Analysis and Modeling: * new RR Distance Maps tool: protein contact maps color-coded by distance (and/or std dev, if comparing structures) * update to AmberTools 14 (new force field options) * Multalign Viewer sequence alignment window: - can plot backbone and all-atom RMSDs, not just CA-RMSDs - show feature annotations from NCBI Conserved Domain Database - search by full or partial sequence name * structure-derived amino acid substitution matrices SDM, HSDM (more choices for sequence alignment and conservation calcs) * Modeller options: thorough optimization, distance restraints * "mda" command (MultiDomain Assembler): - shows BLAST alignment in Multalign Viewer - provides more options for template selection - calls Modeller dialog Volume Data (density maps, electrostatic potential): * "vop" command new options: take pointwise minimum of two or more maps, skeletonize, normalize density maps * "vseries measure" to track isosurface area, enclosed volume, and centroid position across time series Enjoy! On behalf of the Chimera team, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco From owner-chemistry@ccl.net Thu Nov 6 16:30:00 2014 From: "Mark Berger mberger]~[nvidia.com" To: CCL Subject: CCL: Live Webinar on Nov. 11 Heterogeneous CPU+GPU Molecular Dynamics wit Message-Id: <-50710-141106160703-5611-ACmfJyx2cosa2xrBDjPePw#server.ccl.net> X-Original-From: "Mark Berger" Date: Thu, 6 Nov 2014 16:07:02 -0500 Sent to CCL by: "Mark Berger" [mberger##nvidia.com] Register for the CHARMM Webinars & Live Q&A on Tuesday, November 11, 2014 9:00 AM Pacific Standard Time. CHARMM is a versatile and widely used molecular simulation program with broad application to many-particle systems. In this live webinar the performance and accuracy of the heterogeneous CPU+GPU Molecular Dynamics (MD) in CHARMM will be highlighted. The GPU is used for the direct part of forces and the CPU computes all other contributions (reciprocal, bonded, SHAKE, etc.). Click below for full description and registration. Space is limited. Heterogeneous CPU+GPU Molecular Dynamics engine in CHARMM with Biofuels Applications Tuesday, November 11, 2014 9:00 AM Pacific Standard Time https://www2.gotomeeting.com/register/965881002 Presenters: Antti-Pekka Hynninen, Ph.D., Research Scientist, NREL: https://www.nrel.gov/energysciences/biosciences/staff/antti_pekka_hynnine n Michael Crowley, Ph.D., Principal Scientist, NREL: https://www.nrel.gov/energysciences/biosciences/staff/michael_crowley We look forward to seeing you. Please share this valuable webinar with your friends and colleagues. If youre unable to attend the live webinar with Q&A, register to gain access to the recording. Mark Berger mberger^nvidia.com