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Computational Chemistry HighlightsImportant recent papers in computational and theoretical chemistry <br>A free resource for scientists run by scientists
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Computational Chemistry Highlights | compchemhighlights.org Reviews
https://compchemhighlights.org
Important recent papers in computational and theoretical chemistry <br>A free resource for scientists run by scientists
compchemhighlights.org
Computational Chemistry Highlights: Big Data Meets Quantum Chemistry Approximations: The ∆-Machine Learning Approach
http://www.compchemhighlights.org/2015/04/big-data-meets-quantum-chemistry.html
Important recent papers in computational and theoretical chemistry. A free resource for scientists run by scientists. Sunday, April 26, 2015. Big Data Meets Quantum Chemistry Approximations: The ∆-Machine Learning Approach. Pavlo O. Dral,. And O Anatole von Lilienfeld Journal of Chemical Theory and Computation. Contributed by Jan Jensen. H t(R t) approx Delta b t(R b) = E b(R b) sum {i=1} N alpha i e { R i-R b / sigma}$. A Coulomb matrix ($ mathbf{C}$) is constructed for each molecule. Where $r {kl}$ is ...
Computational Chemistry Highlights: Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics
http://www.compchemhighlights.org/2015/05/using-dispersion-corrected-density.html
Important recent papers in computational and theoretical chemistry. A free resource for scientists run by scientists. Thursday, May 14, 2015. Using dispersion-corrected density functional theory to understand supramolecular binding thermodynamics. Antony, J. Sure, R. Grimme, S. Chem. Commun. 2015, 51, 1764-1774. Contributed by Steven Bachrach. Reposted from Computational Organic Chemistry. Grimme and coworkers have a featured article on computing host-guest complexes in a recent ChemComm. And the related...
Computational Chemistry Highlights: Electron-Driven Proton Transfer Along H2O Wires Enables Photorelaxation of πσ* States in Chromophore−Water Clusters
http://www.compchemhighlights.org/2015/04/electron-driven-proton-transfer-along-h.html
Important recent papers in computational and theoretical chemistry. A free resource for scientists run by scientists. Wednesday, April 22, 2015. Electron-Driven Proton Transfer Along H. O Wires Enables Photorelaxation of πσ* States in Chromophore−Water Clusters. More than just shifting state energies, polar solvents may actively participate in the photochemistry of excited molecules. Szabla, R. Šponer, J. Góra, R. W. J. Phys. Chem. Lett. 2015, 6, 1467-1471. Highlighted by Mario Barbatti. Hypothesis has b...
Computational Chemistry Highlights: Editorial Board
http://www.compchemhighlights.org/p/editorial-board.html
Important recent papers in computational and theoretical chemistry. A free resource for scientists run by scientists. Department of Chemistry and Chemical Biology, Harvard University, USA [ twitter. Department of Chemistry, Trinity University, Texas, USA [ blog. Max Planck Institute for Coal Research, Germany [ twitter. Department of Medicinal Chemistry, University of Utah, USA Highlights. London Centre for Nanotechnology, University College London, UK [ blog. Thomas R. Cundari. Dmitri G. Fedorov. Depart...
Computational Chemistry Highlights: Uthrene, a radically new molecule?
http://www.compchemhighlights.org/2015/05/uthrene-radically-new-molecule.html
Important recent papers in computational and theoretical chemistry. A free resource for scientists run by scientists. Wednesday, May 6, 2015. Uthrene, a radically new molecule? Melle-Franco, M. "Uthrene, a radically new molecule? 2015, 51, 5387-5390. Contributed by Steven Bachrach. Reposted from Computational Organic Chemistry. Is the smallest formally diradical fragment of graphene; it cannot be expressed in a closed shell, fully electron-paired Kekule form. Its isomer zethrene 2. Is 165 kcal mol. 1) Me...
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molecularmodelingbasics.blogspot.com
Molecular Modeling Basics: GAMESS, memory and parallel
http://molecularmodelingbasics.blogspot.com/2009/08/gamess-memory-and-parallel_20.html
The "how to" of molecular modeling in education and research. Thursday, August 20, 2009. GAMESS, memory and parallel. The screencast above is a repeat from the last post. In this post I discuss the basics of GAMESS memory requirements. The simplest case is when you are not running in parallel, i.e. the number of processors in GAMESSQ is set to 1, so I discuss this case first. 1 Memory is specified in $system, and the default is 1 mega-word (i.e. 1,000,000 words):. 4 Here is the simplest way to deal with ...
Postdoc position open in my group - FX's blog: musings on chemistry, among other things…
http://blog.coudert.name/post/2015/02/02/Postdoc-position-open-in-my-group
FX's blog: musings on chemistry, among other things. 171; Why correcting the scientific record is hard. Tired of issues , concerns and worrying signs. Postdoc position open in my group. On Monday 2 February 2015, 22:10 - Permalink. I'm happy to announce there is an open postdoc position in my research group. Rational Design of Framework Materials with Tailored Mechanical and Thermal Properties: A Combined Physics/Chemistry Approach. Part of a collaboration between myself ( François-Xavier Coudert.
proteinsandwavefunctions.blogspot.com
Proteins and Wave Functions: Python peer instruction questions
http://proteinsandwavefunctions.blogspot.com/2015/05/python-peer-instruction-questions.html
Proteins and Wave Functions. Science in the open. Sunday, May 10, 2015. Python peer instruction questions. I am teaching a molecular simulations/intro to python course and have just finished drafting the last sets of peer instruction questions. Here's the last question. The idea is that they have to write a small python program on the spot but this might be more of a take home question. Can you do it? I'm not always this "evil". Here's a more typical one. This work is licensed under a. And here is the li...
proteinsandwavefunctions.blogspot.com
Proteins and Wave Functions: Selecting full residues within a certain distance of another residue or atom in PyMOL
http://proteinsandwavefunctions.blogspot.com/2015/03/selecting-full-residues-within-certain.html
Proteins and Wave Functions. Science in the open. Saturday, March 28, 2015. Selecting full residues within a certain distance of another residue or atom in PyMOL. To select all atoms in a residue (plus any HETATMs) that is within 3 Å of any atom in residue 63 type:. Select br. all within 3 of resi 63. To select all atoms in a residue (plus any HETATMs) that is within 3 Å of the CA atom in residue 63 type:. Select br. all within 3 of 63/CA. If you want to name the selection type. Posted by Jan Jensen.
proteinsandwavefunctions.blogspot.com
Proteins and Wave Functions: If I deposit a pre-print on arXiv or Nature Precedings where can I submit my paper?
http://proteinsandwavefunctions.blogspot.com/2012/02/if-i-deposit-pre-print-on-arxiv-or.html
Proteins and Wave Functions. Science in the open. Monday, February 27, 2012. If I deposit a pre-print on arXiv or Nature Precedings where can I submit my paper? When we submitted our last paper for publication. We also posted the manuscript on the pre-print server arXiv. This has several advantages:. 1) It makes the work freely accessible to everyone while the paper is being reviewed. 2) It makes the work freely accessible to everyone after its been published. 3) It establishes priority. I wasn't sure ex...
proteinsandwavefunctions.blogspot.com
Proteins and Wave Functions: Bachelor Projects
http://proteinsandwavefunctions.blogspot.com/p/bachelor-projects.html
Proteins and Wave Functions. Science in the open. A predictive model for H/D exchange rates in proteins (7.5 or 15 ECTS). Predicting the CD spectrum of proteins (7.5 or 15 ECTS). Evaluation of fragment based methods and semi-empirical methods of ligand binding in cyclodextrines (7.5 ECTS). Implementation of the pair interaction decomposition analysis in the EFMO method (15 ECTS). Training a Bayesian network using quantum chemical NMR data for fast prediction of protein NMR (7.5 or 15 ECTS). And here is t...
SoftSimu blogs: Molecular crowding effects on disordered proteins dynamics
http://softsimu.blogspot.com/2013/03/v-behaviorurldefaultvmlo.html
The blogspace of SoftSimu. The views expressed in this blog are entirely those of the authors as listed per posting and do not represent those of our respective universities or other employers. SoftSimu on the web. Thursday, 14 March 2013. Molecular crowding effects on disordered proteins dynamics. Cino EA, Karttunen M, Choy WY (2012) Effects of molecular crowding on the dynamics of intrinsically disordered proteins. PLoS One. 7:e49876. link to manuscript. Fig 2 Differential dynamics between disordered a...
Jose L. Mendoza-Cortes
http://mendoza.eng.fsu.edu/links.html
Our website at Scientific Computing. Our website at the Materials Institute. Our team in Condensed Matter at the MagLab. Richard Hamming: "You and Your Research". Data Visualization (DataViz) tools:. Http:/ vis.stanford.edu/wrangler/. Powering the World with Zero Carbon Emissions and Solar Power infographic. The Future of Solar Energy infographic. Automobiles and the Environment infographic. Unexpected Beauty of Science. 42 is the "Answer to the Ultimate Question". Magnificent Eruption in the sun.
computerandchemistry.blogspot.com
Comp and Chem: Calculate RMSD from two XYZ files
http://computerandchemistry.blogspot.com/2013/04/calculate-rmsd-from-two-xyz-files.html
Masters student in Computational Chemistry at University of Copenhagen, writing about what I feel like. Enjoy the reading. Friday, 26 April 2013. Calculate RMSD from two XYZ files. Calculating the RMSD mathematically for two sets of xyz coordinates for $n$ particles is straight forward:. Mathrm{RMSD}(v,w) = sqrt{ frac{1}{n} sum {i=1} n ( v {ix} - w {ix}) 2 (v {iy} - w {iy}) 2 (v {iz} - w {iz}) 2 ) }$. Http:/ en.wikipedia.org/wiki/Kabsch algorithm. The algorithm is nicely written out on wikipedia, so it w...
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Molecular Quantum Dynamics Research Group. On the emergence of molecular structure. Tunneling splittings from symmetrized PIMD. Numerically-constructed kinetic energy operators. Rovibrational transitions of the methane-water dimer. We seek talented candidates who are interested in joining the group at the doctoral level! We also offer a range of Bachelor and Master projects! Quantum Dynamics Meetings in Budapest (2018). Our group participates at the AMOC. Pázmány Péter sétány 1/A. 1117 Budapest, Hungary.
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Computational Chemistry Highlights
Important recent papers in computational and theoretical chemistry. A free resource for scientists run by scientists. Wednesday, March 14, 2018. DeePCG: A Deep Neutral Network Molecular Force Field. DeePCG: constructing coarse-grained models via deep neural networks. L Zhang, J Han, H Wang, R Car, Weinan E. arXiv:1802.08549v2. Contributed by Jesper Madsen. And Zhang et al.[3] take advantage of similar ideas. Zhang et al. simulate liquid water using ab initio. FF transferability, however, is likely where ...
Comp Chem Kitchen | Computational Chemistry in Oxford
Computational Chemistry in Oxford. Tools & Resources. November 19, 2016. Kitchen for computational chemists, cheminformaticians, and molecular modelers will be on. Th, 2017, at 5.00 pm. In the Abbot’s Kitchen in the Inorganic Chemistry Laboratory. Our main speaker will be: Dr Russell Viner from Syngenta, UK. Structure-Based Design of a Novel Class of Herbicidal HPPD Inhibitors. You can register here. Refreshments will be provided. We will also have a lightning talk:. Anthony Bradley (Chemistry / DLS).
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