lect23-applications

lect23-applications - Notes ! Group Project presentations...

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CMSC 714 Lecture 23 Applications Alan Sussman 2 Notes ! Group Project presentations next Tuesday/Thursday – email sent with (approximate) schedule – final report due Wed., Dec. 14 ! Course evaluation web site open – http://www.CourseEvalUM.umd.edu ! Exam returned today – Average: 73 Median: 76 25%: 63 75%: 85 3 Anton ! Special purpose machine built for molecular dynamics simulations, built at D.E. Shaw Research – to simulate biological processes that occur on very small time scales (10 -15 sec), such as protein folding, interaction between proteins, etc. – and simulate those processes for a long time ! Molecular dynamics – force calculation followed by integration step to move particles – biomolecular forces have 3 parts • bonded forces – small atomic groups with covalent bonds • van der Waals forces – all pairs of atoms, but fall off quickly with distance (so only need close ones) • electrostatic forces – all pairs of atoms, fall off slowly with distance – divide into 2 parts to avoid all pairs computation 4 Anton ! Anton machine up to 512 nodes in 8x8x8 torus each node has 2 parts on 1 chip high throughput interaction subsystem (HTIS) for range-limited interactions , using 32 hardwired pairwise point interaction pipelines (PPIPs)
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This note was uploaded on 01/12/2012 for the course CMSC 714 taught by Professor Staff during the Fall '07 term at Maryland.

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lect23-applications - Notes ! Group Project presentations...

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