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Molecular Modeling BasicsThe "how to" of molecular modeling in education and research
http://molecularmodelingbasics.blogspot.com/
The "how to" of molecular modeling in education and research
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Molecular Modeling Basics | molecularmodelingbasics.blogspot.com Reviews
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The "how to" of molecular modeling in education and research
molecularmodelingbasics.blogspot.com
Molecular Modeling Basics: Tunneling and STM
http://molecularmodelingbasics.blogspot.com/2009/09/tunneling-and-stm.html
The "how to" of molecular modeling in education and research. Saturday, September 26, 2009. A few weeks ago, I gave a guest lecture (read: "I am at a conference that day, could you do it for me? In a course entitled Unifying Concepts in Nanoscience. The topic was basic quantum mechanics (chapter 9 and a bit of 10 in Atkin's Physical Chemistry): particle in a box, etc. These days, the first thing I do when preparing a lecture is to scour Molecular Workbench. Note: you need to install MW. Errors in the book.
Molecular Modeling Basics: Virtual Molecular Modeling Kit
http://molecularmodelingbasics.blogspot.com/2012/04/virtual-molecular-modeling-kit.html
The "how to" of molecular modeling in education and research. Sunday, April 15, 2012. Virtual Molecular Modeling Kit. I recently came across a very interesting resource called the Virtual Molecular Modeling Kit. It looks like it can do an awful lots of things and I have only scratched the surface myself. Very commendably, the authors Otis Rothenberger. And Thomas Newton, have created a set of instructional videos. The video below highlights the fact Jmol. These, and related sites such as this one. I am a...
Molecular Modeling Basics: A very brief introduction to the electron correlation energy
http://molecularmodelingbasics.blogspot.com/2015/08/the-electron-correlation-energy.html
The "how to" of molecular modeling in education and research. Sunday, August 9, 2015. A very brief introduction to the electron correlation energy. RHF is often not accurate enough for predicting the change in energies due to a chemical reaction, no matter how big a basis set we use. The reason is the error due to the molecular orbital approximation. Psi ({ bf{r} 1},{ bf{r} 2}, ldots { bf{r} N}) approx sum limits {i = 1} L { C i}{ Phi i}({ bf{r} 1},{ bf{r} 2}, ldots { bf{r} N})} $. Psi approx {C 0}{ Phi ...
Molecular Modeling Basics: The Molecular Modeling Basics Electronic Color Supplement
http://molecularmodelingbasics.blogspot.com/2011/03/molecular-modeling-basics-electronic.html
The "how to" of molecular modeling in education and research. Saturday, March 5, 2011. The Molecular Modeling Basics Electronic Color Supplement. A) RHF/6-31G(d) 0.002 au isodensity surface with superimposed electrostatic potential for (a) cis-HO(H)C=C(H)OH and (b) cis-CH. And In both cases, the maximum potential value is 0.05 au. From page 79 of Molecular Modeling Basics. Figure 3.5 shows such plots for cis-CH. As I wrote on the blog. As suggested by Henry Rzepa whose ebooks and wiki how-to. Almost all ...
Molecular Modeling Basics: Finding a transition state: an Sn2 reaction
http://molecularmodelingbasics.blogspot.com/2009/08/finding-transition-state-sn2-reaction.html
The "how to" of molecular modeling in education and research. Sunday, August 2, 2009. Finding a transition state: an Sn2 reaction. Here is a screencast I made about finding a transition state for the reaction. The general approach is as follows. 1 Build the structure (F. 2 Optimize the geometry while constraining a key distance (between the F and C atom) to a certain value (2.0 Å). 3 Compute the frequencies for the optimized geometry to check for an imaginary frequency. The key question is of course why ...
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Computational Biochemistry: January 2014
http://combichem.blogspot.com/2014_01_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Thursday, January 2, 2014. FragBuilder: Setting up a scan of peptide conformations. This post covers the essentials of how to set up a scan of different peptide conformations. We have used this method to calculate more than 1.5M QM calculation on model peptides in our group. In this example we make a tri-glycine peptide and scan over the phi/psi torsion angles between -180 and 180 degrees with 60 degrees spacing. Subscribe to: Pos...
О.Лхагва багшийн физик-философи: October 2013
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ОЛхагва багшийн блог. Философийн өгүүлэлүүд, эрдэм шинжилгээний ажлаас. olhagvao@yahoo.com; 976-99167676. Monday, October 7, 2013. 8220;Цацрагийн биологи, цацрагийн хамгаалал”сэдэвт олон улсын эрдмийн бага хурал болж өнгөрлөө. 8220; Цацрагийн биологи, цацрагийн хамгаалал”сэдэвт. Олон улсын эрдмийн бага хурал. Монгол улс, Цөмийн шинжилгээний нэгдсэн институтийн. Ийн Цацрагийн биологийн лаборатори. МУИС-ийн Физик электроникийн сургууль. ШУТ Сан дэмжиж, проф. О. Лхагва хөтлөн зохион байгууллаа. ЦБЛ –и...
Computational Biochemistry: August 2013
http://combichem.blogspot.com/2013_08_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Tuesday, August 27, 2013. Aligning PDB structures with Biopython. You can use the Bio.PDB module in Biopython to align PDB files. This is how I did it. The code should be pretty much self-explanatory. In this example I align the crystal structure of Ubiquitin (PDB code: 1UBQ) to the first structure of a corresponding NMR ensemble (PDB code: 1D3Z, see picture below). Posted by Anders Steen Christensen. Friday, August 16, 2013.
Computational Biochemistry: May 2013
http://combichem.blogspot.com/2013_05_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Tuesday, May 28, 2013. Calculating Diffusion Coefficients from Random Walk Monte Carlo. This is taken from a lecture I gave during the Molecular Statistics course at University of Copenhagen, which I co-teach with Jan Jensen and Jimmy Kromann. The students have to program different types of molecular simulations and are not expected to have any programming experience before the course. The equations of motion are shown here:.
Computational Biochemistry: Automatic mounting of remote storage via SSHFS on Amazon EC2 instances
http://combichem.blogspot.com/2014/02/automatic-mounting-of-remote-storage.html
Computational molecular sciences and free software. Pirates and molecules! Wednesday, February 19, 2014. Automatic mounting of remote storage via SSHFS on Amazon EC2 instances. In this blog I demonstrate how you can create an Amazon EC2 instance image that will automount a folder on a remote server via SSHFS. The purpose here is to fire up a EC2 compute server, run a program and save the output from that program on our local compute cluster at the university. An Amazon EC2 instance with sshfs installed.
Computational Biochemistry: March 2013
http://combichem.blogspot.com/2013_03_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Friday, March 1, 2013. For single point energies). I am looking at the conversion of chorismate to prephenate in Chorismate Mutase, to benchmark a hacky EFMO-RHF:MP2 method we've implemented in our group. Casper Steinmann did an adiabatic mapping of the reaction path, and we though it'd be cool to do coupled cluster single point energies on snapshots from the reaction path and some something ONIOM style. C 42243912717439 56.98...
Computational Biochemistry: August 2012
http://combichem.blogspot.com/2012_08_01_archive.html
Computational molecular sciences and free software. Pirates and molecules! Tuesday, August 28, 2012. Displaying disagreements in protein structures. I recently made a post. On how to color a protein structure by disagreements between experimental chemical shifts and chemical shifts predicted from the structure. Here is another way to display these kinds of errors, which I also find quite nice. Atoms radii are scaled proportionally the error in predicted chemical shifts. 4), pp 1480–1492. Svn checkout htt...
О.Лхагва багшийн физик-философи: December 2009
http://num-spe303.blogspot.com/2009_12_01_archive.html
ОЛхагва багшийн блог. Философийн өгүүлэлүүд, эрдэм шинжилгээний ажлаас. olhagvao@yahoo.com; 976-99167676. Friday, December 25, 2009. Нано-онолын тооцоо, судалгааны ажил явагдаж байгаа. Нүүрстөрөгчийн атомаас тогтох балчулуун хуудас, түүнээс үүсгэсэн фуллерен, наногуурс, конус болон гиперболойд, тоорцогт наногуурс, нанотууз,. Наношоо мэтийн муруй топологи. Судалгаанд математик тооцооны програм, кавнт химийн багц програмуудыг ашигладаг. Тооцооны зарим үр дүнгээс:. Subscribe to: Posts (Atom). A beginners gu...
О.Лхагва багшийн физик-философи: June 2010
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ОЛхагва багшийн блог. Философийн өгүүлэлүүд, эрдэм шинжилгээний ажлаас. olhagvao@yahoo.com; 976-99167676. Tuesday, June 29, 2010. 160;( General Atomic and Molecular Electronic Structure System. Молекул, нанобөөмийн бүтэц, шинж чанарыг тооцоо, зураглалаар дүрслэн. Босгодог квант физик-химийн багц програм юм. Элхийн томоохон сургуулиудын сургалт- судалгаа, эрдэм шинжилгээнд нэвтэрсэн . GAMESS лабораторыг манай улсын их сургуулиудын. Нэртэй гарын авлагыг бэлтгэжээ. Subscribe to: Posts (Atom).
О.Лхагва багшийн физик-философи: January 2010
http://num-spe303.blogspot.com/2010_01_01_archive.html
ОЛхагва багшийн блог. Философийн өгүүлэлүүд, эрдэм шинжилгээний ажлаас. olhagvao@yahoo.com; 976-99167676. Monday, January 25, 2010. Физмат ШУ доктор, проф. О. Лхагва,. Шинжлэх ухааны гавьяат зүтгэлтэн. Монголы различали материальное “голубое” небо от духовного “вечного” неба.Небо монголы представляли правителем мира, вечным правосудием и источником жизни.“Вечное небо” небыло личным богом, а лишь мировым порядком. Tuesday, January 19, 2010. Доктор физико-математических наук, проф. О. Лхагва*. Квант физик ...
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Molecular Models Company Home Page
2843 S. Bartells Dr. Beloit, WI 53511 Phone: (608) 884.9877. Enter your search string and click the Go button. Where to Buy Online. Molecules in a Bag. Welcome to Molecular Models Company. And sets in the world. All of our molecular model sets, kits and individual expansion components are color coded. We are always looking for ways to better meet the needs of our valued customers. If you do not find what you are looking for in our stock sets and kits, please drop us an email. 160; With our custom.
Molecular Models Company Home Page
2843 S. Bartells Dr. Beloit, WI 53511 Phone: (608) 884.9877. Enter your search string and click the Go button. Where to Buy Online. Molecules in a Bag. Welcome to Molecular Models Company. And sets in the world. All of our molecular model sets, kits and individual expansion components are color coded. We are always looking for ways to better meet the needs of our valued customers. If you do not find what you are looking for in our stock sets and kits, please drop us an email. 160; With our custom.
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computational chemistry
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Molecular Modeling Basics
The "how to" of molecular modeling in education and research. Sunday, April 1, 2018. Computational Chemistry Highlight: March issue. The March issue of Computational Chemistry Highlights. CCH is an overlay journal. That identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is a free resource run by scientists for scientists. You can read more about it here. Posted by Jan Jensen. Links to this post.
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molecularsimulation.org | the web portal for molecular simulation
The web portal for molecular simulation. Molecular Dynamics Simulations of Capillary Rise Experiments in Nanotubes Coated with Polymer Brushes. By site admin - Posted on February 12th, 2008. Bull; polymer brushes. Dimitrov, D.I. Langmuir, Volume 24, Number 4, p.1232-1239 (2008). Http:/ dx.doi.org/10.1021/la7019445. Bull; 896 reads. ReaxFF Reactive Force Field for Molecular Dynamics Simulations of Hydrocarbon Oxidation. By site admin - Posted on February 12th, 2008. Bull; Chemical reactions. Sheu, S.Y.
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