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- | ===== High-performance simulation of large bimolecular systems - NAMD ===== | ||
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- | NAMD, recipient of a 2002 Gordon Bell Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code. | ||
- | Documentation and source code on the web page of " | ||
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- | There are few possibilities to start NAMD simulation on the MOGON cluster. | ||
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- | //<PATH TO NAMD INSTALLATION>/ | ||
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- | This starts one threaded simulation direkt on the login host. Input configuration file describes simulation. Complete description of the input file format is available in the [[http:// | ||
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- | Using threaded start allows to achieve performance increasing: | ||
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- | //bsub -R " | ||
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- | where <number of threads> is normally equal to <number of cores>. | ||
- | For example | ||
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- | //bsub -R " | ||
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- | starts NAMD simulation with 16 threads using 16 cores of a node. | ||
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- | Mogon cluster contains different nodes with up to 64 cores. | ||
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- | On machines with more than 32 cores it may be necessary to add a communication thread and run on one fewer core than the machine has. For example on a 64-core machine this would be run as | ||
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- | //bsub -R " | ||
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- | === Memory Usage === | ||
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- | NAMD has traditionally used less than 100MB of memory even for systems | ||
- | of 100,000 atoms. |