Temperature coupling parameters

NAMD is capable of performing temperature coupling, in which forces are added or reduced to simulate the coupling of the system to a heat bath of a specified temperature. This capability is based on that implemented in X-PLOR which is detailed in the X-PLOR User's Manual [6].

• tCouple $\langle$ perform temperature coupling? $\rangle$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not temperature coupling is active. If set to on, then the parameter tCoupleTemp must be set and the parameters tCoupleFile and tCoupleCol can optionally be set to control the behavior of this feature.

• tCoupleTemp $\langle$ temperature for heat bath (K) $\rangle$
  Acceptable Values: positive decimal
  Description: Temperature to which atoms affected by temperature coupling will be adjusted. This temperature will be roughly maintained across the affected atoms through the addition of forces.

• tCoupleFile $\langle$ PDB file with tCouple parameters $\rangle$
  Acceptable Values: UNIX filename
  Default Value: coordinates
  Description: PDB file to use for the temperature coupling coefficient for each atom. If this parameter is not specified, then the PDB file specified by coordinates is used.

• tCoupleCol $\langle$ column of PDB from which to read coefficients $\rangle$
  Acceptable Values: X, Y, Z, O, or B
  Default Value: O
  Description: Column of the PDB file to use for the temperature coupling coefficient for each atom. This value can be read from any floating point column of the PDB file. A value of 0 indicates that the atom will remain unaffected.