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High-performance simulation of large bimolecular systems - NAMD

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.1525446871.txt.gz · Last modified: 2018/05/04 17:14 by noskov