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namd [2018/05/04 17:13]
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-===== High-performance simulation of large bimolecular systems - NAMD ===== 
-<WRAP center round todo 90%> 
-''This page is outdated. We hope to provide more information, soon.'' 
-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 "[[|Theoretical and computational biophysics group]]" 
-There are few possibilities to start NAMD simulation on the MOGON cluster. 
-//<PATH TO NAMD INSTALLATION>/namd2 <input configuration file>// 
-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 [[|NAMD Documentation]]. 
-=== Memory Usage === 
-NAMD has traditionally used less than 100MB of memory even for systems 
-of 100,000 atoms.  With the reintroduction of pairlists in NAMD 2.5, however, memory usage for a 100,000 atom system with a 12A cutoff can approach 300MB, and will grow with the cube of the cutoff.  This extra memory is distributed across processors during a parallel run, but a single workstation may run out of physical memory with a large system. 
  • namd.1525446801.txt.gz
  • Last modified: 2018/05/04 17:13
  • by noskov