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Domain: accelrys.com

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Comments · 6

  1. Re:VMD is pretty cool by cashman73 · · Score: 1 · on Chemistry Tasks For the Computer Lab?
    I'll agree that VMD is something that is definitely worth teaching about. It's free, and easy to install and use on a variety of platforms. I'd also recommend introducing them to the Protein Data Bank, which is a free database of x-ray/nmr structures of proteins. Though it gets a bit more into biochemistry and molecular biology from a basic high school chemistry course, some of the simpler structures available there would give a student a good introduction to some of the applications of computational chemistry.

    While most of the professional molecular modeling software (InsightII, Sybyl, MOE, etc) will likely be out of the price range of a high school course, ArgusLab is free and pretty decent for some basic small molecule type stuff. The Accelrys Discovery Studio Visualizer is a freely-available version of Discovery Studio, which is also pretty decent. There's a Windows and Linux version of this.

    Depending on how advanced your students are, you may want to introduce them to some molecular dynamics. NAMD is freely-available for Windows/Linux/Mac, and there are some good tutorials available. However, this might be getting a bit too advanced for a basic high school course, and might be a bit better to introduce at the undergraduate/graduate level. For most high school students, I'd probably teach them the basics would ArgusLab first.

  2. Re:We just need an alternative to X by fritsd · · Score: 1 · on Kernel 2.6.31 To Speed Up Linux Desktop

    Visualisation of the 3-D structure of medium-sized molecules, for example. See picture on this advertisement. That was 20 years ago, on an SGI Iris. The workstation was slow but fast enough to watch your basepairs of DNA in 3-D with OpenGL. I can't recall the specs of the Iris. Later we also used a faster SGI Indy which (I just looked up on wikipedia) had something like 32 Mb memory and ran on a MIPS R4400 CPU at (guessing wildly here) 200 MHz.

  3. molecular modeling comparison by cashman73 · · Score: 0, Offtopic · on Autodesk Suing to Keep Format Closed
    Never used AutoCAD, so I could care less whether it's got a proprietary file format or not. In drug design and molecular modeling, the two most commonly used software programs for 3-D modeling are Sybyl and Insight II. Sybyl's native file format is mol2 , and Insight II's is car/mdf . Both programs also fully support the industry standard pdb format. All three files are simple text files, nothing proprietary about them. Insight II will write a mol2 file with no problems, and vice versa. There are also several third party applications that handle and read/write mol2 and car/mdf files. Nobody's really complaining.

  4. The Obvious Solution by Frumious+Wombat · · Score: 3, Informative · on Organizing Organic Chemical Reactions?

    (from someone who teaches Chemistry for a living)

    You're taking your courses in the wrong order. You need P-Chem and Inorganic to understand _why_ Organic works. Once you can understand which way the electrons flow, you're halfway done. Look for Woodward and Hoffman's book on orbital symmetry interactions, and the old Ian Fleming (different one) "Frontier Orbitals and Organic Chemical Reactions". Albright, Burdett, Whangbo, "Orbital Interactions in Chemistry" is also a good general source, though it's rather inorganic in focus.

    The other half is to actually memorize 2000 reactions, if you're going to be a professional organic chemist. You have to know solvent, temperature, and related reactions. You need to know how mechanisms work, what transition states look like, and how both steric and electronic effects interact. To this you can add metal-mediated transformations (organometallic). This is why organic (so say my female colleagues) is overwhelmingly male; the same ability that makes you able to remember 2000 random movie quotes or baseball statistics allows you to memorize organic reactions instead.

    Take a deep breath, and start making flash cards. Remember, Organic is just Inorganic with boring elements.

    As to the software question, CambridgeSoft (http://www.cambridgesoft.com/ and Accelrys (http://www.accelrys.com/ are two examples of people with expert systems that do some of what you're asking. You will not like the price.

  5. Re:Obvious Link? by joeljkp · · Score: 1 · on 25th TOP500 List Released

    Molecular dynamics with Discover

  6. Security by akuma(x86) · · Score: 1 · on Bioinformatics in The Economist

    Perhaps some of these bioinformation engineers should spend a little time on security. I tried to go to the website of one of the companies referenced in the Economist article and got a defaced website: