NAMD configuration parameters

This section describes the various configuration parameters that are available with NAMD. It is broken into subsections that group similar parameters together. The following parameters are required for every NAMD simulation:

• numsteps (page ),

• coordinates (page ),

• structure (page ),

• parameters (page ),

• exclude (page ),

• outputname (page ),

• either cutoff (page ) or both of eleccutoff (page ) and vdwcutoff (page ),

• one of the following three:
  • temperature (page ),

  • velocities (page ),

  • binvelocities (page ).

These required parameters specify the most basic properties of the simulation. In addition, it is highly recommended that

• pairlistdist be specified with a value at least one greater than the maximum of cutoff, vdwcutoff, and eleccutoff,
• stepspercycle be chosen so that the product of stepspercycle and timestep does not exceed 4.0 unless rigidBonds all is specified, in which case the upper limit is perhaps doubled.