Temperature Control and Equilibration

Langevin dynamics parameters

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 [10], although a different integrator is used.

• langevin $<$ use Langevin dynamics? $>$
  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.

• langevinTemp $<$ temperature for Langevin calculations (K) $>$
  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.

• langevinDamping $<$ damping coefficient for Langevin dynamics (1/ps) $>$
  Acceptable Values: positive decimal
  Default Value: per-atom values from PDB file
  Description: Langevin coupling coefficient to be applied to all atoms (unless langevinHydrogen is off, in which case only non-hydrogen atoms are affected). If not given, a PDB file is used to obtain coefficients for each atom (see langevinFile and langevinCol below).

• langevinHydrogen $<$ Apply Langevin dynamics to hydrogen atoms? $>$
  Acceptable Values: on or off
  Default Value: on
  Description: If langevinDamping is set then setting langevinHydrogen to off will turn off Langevin dynamics for hydrogen atoms. This parameter has no effect if Langevin coupling coefficients are read from a PDB file.

• langevinFile $<$ PDB file containing Langevin parameters $>$
  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 $<$ column of PDB from which to read coefficients $>$
  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.

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 [10].

• tCouple $<$ perform temperature coupling? $>$
  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 $<$ temperature for heat bath (K) $>$
  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 $<$ PDB file with tCouple parameters $>$
  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 $<$ column of PDB from which to read coefficients $>$
  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.

Temperature rescaling parameters

NAMD allows equilibration of a system by means of temperature rescaling. Using this method, all of the velocities in the system are periodically rescaled so that the entire system is set to the desired temperature. The following parameters specify how often and to what temperature this rescaling is performed.

• rescaleFreq $<$ number of timesteps between temperature rescaling $>$
  Acceptable Values: positive integer
  Description: The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature rescaling. If this value is given, then the rescaleTemp parameter must also be given to specify the target temperature.

• rescaleTemp $<$ temperature for equilibration (K) $>$
  Acceptable Values: positive decimal
  Description: The temperature to which all velocities will be rescaled every rescaleFreq timesteps. This parameter is valid only if rescaleFreq has been set.

Temperature reassignment parameters

NAMD allows equilibration of a system by means of temperature reassignment. Using this method, all of the velocities in the system are periodically reassigned so that the entire system is set to the desired temperature. The following parameters specify how often and to what temperature this reassignment is performed.

• reassignFreq $<$ number of timesteps between temperature reassignment $>$
  Acceptable Values: positive integer
  Description: The equilibration feature of NAMD is activated by specifying the number of timesteps between each temperature reassignment. If this value is given, then the reassignTemp parameter must also be given to specify the target temperature.

• reassignTemp $<$ temperature for equilibration (K) $>$
  Acceptable Values: positive decimal
  Default Value: temperature if set, otherwise none
  Description: The temperature to which all velocities will be reassigned every reassignFreq timesteps. This parameter is valid only if reassignFreq has been set.

• reassignIncr $<$ temperature increment for equilibration (K) $>$
  Acceptable Values: decimal
  Default Value: 0
  Description: In order to allow simulated annealing or other slow heating/cooling protocols, reassignIncr will be added to reassignTemp after each reassignment. (Reassignment is carried out at the first timestep.) The reassignHold parameter may be set to limit the final temperature. This parameter is valid only if reassignFreq has been set.

• reassignHold $<$ holding temperature for equilibration (K) $>$
  Acceptable Values: positive decimal
  Description: The final temperature for reassignment when reassignIncr is set; reassignTemp will be held at this value once it has been reached. This parameter is valid only if reassignIncr has been set.

Lowe-Andersen dynamics parameters

NAMD can perform Lowe-Andersen dynamics, a variation of Andersen dynamics whereby the radial relative velocities of atom pairs are randomly modified based on a thermal distribution. The Lowe-Andersen thermostat is Galilean invariant, therefore conserving momentum, and is thus independent of absolute atom velocities. Forces are applied only between non-bonded, non-hydrogen pairs of atoms. When using rigid bonds, forces are applied to the center of mass of hydrogen groups. The implementation is based on Koopman and Lowe [36].

• loweAndersen $<$ use Lowe-Andersen dynamics? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not Lowe-Andersen dynamics are active. If set to on, then the parameter loweAndersenTemp must be set and the parameters loweAndersenCutoff and loweAndersenRate can optionally be set.

• loweAndersenTemp $<$ temperature for Lowe-Andersen calculations (K) $>$
  Acceptable Values: positive decimal
  Description: Temperature of the distribution used to set radial relative velocities. This determines the target temperature of the system.

• loweAndersenCutoff $<$ cutoff radius for Lowe-Andersen collisions (Å) $>$
  Acceptable Values: positive decimal
  Default Value: 2.7
  Description: Forces are only applied to atoms within this distance of one another.

• loweAndersenRate $<$ rate for Lowe-Andersen collisions (1/ps) $>$
  Acceptable Values: positive decimal
  Default Value: 50
  Description: Determines the probability of a collision between atoms within the cutoff radius. The probability is the rate specified by this keyword times the non-bonded timestep.