The Paul J. Schupf Computational Allure Class amid in the Paul J. Schupf Scientific Computing Center was founded with ability from Colby trustee Paul J. Schupf, grants from the Howard Hughes Medical Institute, and two grants from the National Science Foundation*. The capital compute agent for atomic alternate calculations is an intel based 10 brand compute array the accustomed science compute array . The class has two broadcast clusters one based on seven 8 Amount PowerMacintosh workstations and the added on seven Dell Precision 380 bifold amount 3GHz Windows/Linux systems with 4 GBytes of memory. The software accessible includes atomic orbital, atomic mechanics and dynamics, and chemometric assay software. Acceptance are alien to atomic mechanics calculations in General Allure during their aboriginal year at Colby. The cartoon ability of the workstations in hands-on contest helps alpha acceptance analyze the beheld images in chemistry. They alpha with simple asleep compounds and advance through complicated proteins, Figure 1. In green Organic Allure acceptance use atomic mechanics to abstraction the shapes of molecules by award band lengths and angles from activity minimized structures. Hands-on contest advice acceptance anticipate the energetics of the conformations of arena systems.
In Physical Chemistry, acceptance apprentice the fundamentals of computational chemistry. Weekly appointment contest advise the ability of atomic mechanics, dynamics, and atomic alternate calculations, Figure 2. In PChem, acceptance additionally do class projects that accompaniment the computational contest to accentuate that approach is meant to brighten beginning observations. The accurate ability of atomic mechanics and dynamics is activate in simulation of the motion of molecules in water. These simulations absorb analytic Newton’s equations of motion for abounding hundreds of atoms, Figure 3
In the Biomolecular Anatomy course, acceptance use the cartoon ability of our workstations to accept protein structure, see Figure 1. The acceptance download structures from the Brookhaven Protein Database. They add hydrogens, actuate the minimum activity structure, and abstraction agitator substrate interactions.
In the chief year, acceptance activate to draw access amid their antecedent coursework and their apprentice research. In the Physical Organic course, our acceptance do calculations that affair reactions that are the capacity of their chief analysis projects, Figure 4. We accept absolute apprentice analysis plays a actual important role in undergraduate education, so we anatomy our courses to accommodate the accoutrement and ability for acceptance to become accomplished in research. Teaching through analysis is an important assumption in our curriculum. For example, one of our analysis groups is developing a adjustment to actuate OH radicals in sea-water, Figure 5.
Feel chargeless to download a archetype of the Colby College Atomic Mechanics Tutorial Introduction. Computational contest application atomic mechanics and dynamics are available: Colby College Atomic Mechanics Exercises-MOE tutorial. A adaptation based on QUANTA is additionally available: Colby College Atomic Mechanics Exercises-Quanta version. (Please agenda that antecedent versions of the tutorial accumulated the Tutorial and the Contest in one file.) The CAMD tutorial is an addition to computer aided atomic architecture (pdf format). ( A Microsoft Word adaptation is additionally available: The CAMD tutorial -Word version.) A Ability Point presentation on the basics of CAMD is an addition to CAMD ideas.
A Ability Point presentation on Computer Aided Atomic Architecture and Advice Technology is additionally available. This presentation was presented at the abatement 1998 affair of the Colby-Bowdoin-Bates (CBB) Committee on Technology Use, which is adjourned by the Mellon Foundation.(Many of the slides are repeats of the CAMD presentation, above)
Harold Bell’s Properties of Organic Compounds We now accept ISIS/Base versions of Harold Bell’s Properties of Organic Compounds Database accessible in Windows and Macintosh and SDF architecture versions. This database contains about 5,000 organics with NMR chmical accouterment as absorbed argument to the 2D structures. This database is the base of our Web version: Organic Compounds Database Search.
For added advice on the Computational Allure Class at Colby acquaintance Tom Shattuck at [email protected]
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