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namd [2014/06/17 12:31]
noskov
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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 "[[http://www.ks.uiuc.edu/Research/namd/|Theoretical and computational biophysics group]]" 
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-There are few possibilities to start NAMD simulation on the MOGON cluster. 
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-//<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>// 
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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://www.ks.uiuc.edu/Research/namd/2.9/ug/node9.html|NAMD Documentation]]. 
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-Using threaded start allows to achieve performance increasing: 
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-//bsub -R "affinity[core(<number of cores>)]" <PATH TO NAMD INSTALLATION>/namd2 +p<number of threads> <input configuration file>// 
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-where <number of threads> is normally equal to <number of cores>. 
-For example 
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-//bsub -R "affinity[core(16)]" <PATH TO NAMD INSTALLATION>/namd2 +p 16 <input configuration file>// 
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-starts NAMD simulation with 16 threads using 16 cores of a node. 
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-Mogon cluster consists 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 "affinity[core(64)]" <PATH TO NAMD INSTALLATION>/namd2 +p 63 +commthread <input configuration file>// 
  • namd.1403001075.txt.gz
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