Simulation space partitioning

• eleccutoff $\langle$ local interaction distance for electrostatic calculations (Å) $\rangle$
  Acceptable Values: positive decimal
  Description:  If DPMTA is active, this distance defines the local interaction length for the DPMTA algorithm. Otherwise, this value specifies the distance at which electrostatic interactions are truncated. If eleccutoff is defined, it supersedes cutoff. If eleccutoff is not defined, then cutoff must be defined. See section 4.5 for a further discussion of this configuration value.

• vdwcutoff $\langle$ local interaction distance for van der Waals calculations (Å) $\rangle$
  Acceptable Values: positive decimal
  Description:  This value specifies the distance at which van der Waals interactions are truncated. If vdwcutoff is defined, it supersedes cutoff. If vdwcutoff is not defined, then cutoff must be defined. See section 4.5 for a further discussion of this configuration value.

• cutoff $\langle$ local interaction distance common to both electrostatic and van der Waals calculations (Å) $\rangle$
  Acceptable Values: positive decimal
  Description:  This value can substitute for either eleccutoff or vdwcutoff if either of those is undefined. See section 4.5 for more information.

• switching $\langle$ use switching function? $\rangle$
  Acceptable Values: on or off
  Default Value: off
  Description: If switching is specified to be off, then a truncated cutoff is performed. If switching is turned on, then smoothing functions are applied to both the electrostatics and van der Waals forces. For a complete description of the non-bonded force parameters see section 4.5. If switching is set to on, then switchdist must also be defined.

• elecswitchdist $\langle$ distance at which to activate switching function for electrostatic calculations (Å) $\rangle$
  Acceptable Values: positive decimal $\leq$ eleccutoff
  Description: Distance at which the switching function used to smooth the truncation of electrostatic forces should begin to take effect. This parameter only has meaning if switching is set to on. The value of elecswitchdist must be less than or equal to the value of eleccutoff, since the switching function is only applied on the range from elecswitchdist to eleccutoff. If elecswitchdist is defined, it supersedes switchdist. If elecswitchdist is not defined and switching is on, then switchdist must be defined. For a complete description of the non-bonded force parameters, see section 4.5.

• vdwswitchdist $\langle$ distance at which to activate switching function for van der Waals calculations (Å) $\rangle$
  Acceptable Values: positive decimal $\leq$ vdwcutoff
  Description: Distance at which the switching function used to smooth the truncation of van der Waals forces should begin to take effect. This parameter only has meaning if switching is set to on. The value of vdwswitchdist must be less than or equal to the value of vdwcutoff, since the switching function is only applied on the range from vdwswitchdist to vdwcutoff. If vdwswitchdist is defined, it supersedes switchdist. If vdwswitchdist is not defined and switching is on, then switchdist must be defined. For a complete description of the non-bonded force parameters, see section 4.5.

• switchdist $\langle$ distance at which to activate switching function for electrostatic and van der Waals calculations (Å) $\rangle$
  Acceptable Values: positive decimal $\leq$ cutoff
  Description: Distance at which the switching function should begin to take effect. This parameter only has meaning if switching is set to on. The value of switchdist must be less than or equal to the value of cutoff, since the switching function is only applied on the range from switchdist to cutoff. For a complete description of the non-bonded force parameters see section 4.5.

• pairlistdist $\langle$ distance between pairs for inclusion in pair lists (Å) $\rangle$
  Acceptable Values: positive decimal $\geq$ cutoff
  Default Value: cutoff+1.0
  Description: A pair list is generated each cycle, containing pairs of atoms for which electrostatics and van der Waals interactions will be calculated. This parameter is used when switching is set to on to specify the allowable distance between atoms for inclusion in the pair list. This parameter is equivalent to the X-PLOR parameter CUTNb. If no atom moves more than one-half of pairlistdist-cutoff during one cycle, then there will be no jump in electrostatic or van der Waals energies when the next pair list is built. If pairlistdist is not specified, the value of cutoff+1.0 is used. A value of at least one greater than the maximum of eleccutoff, vdwcutoff, and cutoff is recommended.

• margin $\langle$ extra length in patch dimension (Å) $\rangle$
  Acceptable Values: positive decimal
  Default Value: 1.0
  Description: An internal tuning parameter used in determining the size of the cubes of space with which NAMD uses to partition the system. The value of this parameter will not change the physical results of the simulation. For more details about this parameter see the NAMD Programming Guide. Unless you are very motivated to get the very best possible performance, just leave this value at the default.

• plMarginCheck $\langle$ perform pairlist margin check? $\rangle$
  Acceptable Values: on or off
  Default Value: on
  Description:  If this parameter is activated, a check will be performed during each timestep to detect atoms that may have violated the margin between the pairlistdist and cutoff distances. Such violations will be output by NAMD.