Langevin dynamics parameters

As described in section 5.2.3, NAMD is capable of performing Langevin dynamics, where additional damping and random forces are introduced to the system. This capability is based on that implemented in X-PLOR which is detailed in the X-PLOR User's Manual [6].

• langevin $\langle$ use Langevin dynamics? $\rangle$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not Langevin dynamics active. If set to on, then the parameter langevinTemp must be set and the parameters langevinFile and langevinCol can optionally be set to control the behavior of this feature. Also, rigidBonds must be set to none.

• langevinTemp $\langle$ temperature for Langevin calculations (K) $\rangle$
  Acceptable Values: positive decimal
  Description: Temperature to which atoms affected by Langevin dynamics will be adjusted. This temperature will be roughly maintained across the affected atoms through the addition of friction and random forces.

• langevinFile $\langle$ PDB file containing Langevin parameters $\rangle$
  Acceptable Values: UNIX filename
  Default Value: coordinates
  Description: PDB file to use for the Langevin coupling coefficients for each atom. If this parameter is not specified, then the PDB file specified by coordinates is used.

• langevinCol $\langle$ 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 Langevin coupling coefficients for each atom. The coefficients can be read from any floating point column of the PDB file. A value of 0 indicates that the atom will remain unaffected.