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.
To avoid this, NAMD now provides a pairlistMinProcs config file option that specifies the minimum number of processors that a run must use before pairlists will be enabled (on fewer processors small local pairlists are generated and recycled rather than being saved, the default is ``pairlistMinProcs 1''). This is a per-simulation rather than a compile time option because memory usage is molecule-dependent.
Additional information on reducing memory usage may be found at http://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction