- Langevin dynamics parameters
- Temperature coupling parameters
- Stochastic velocity rescaling parameters
- Temperature rescaling parameters
- Temperature reassignment parameters
- Lowe-Andersen 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* [14],
although a different integrator is used.

use Langevin dynamics?`langevin`**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.temperature for Langevin calculations (K)`langevinTemp`**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.damping coefficient for Langevin dynamics (1/ps)`langevinDamping`**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).Apply Langevin dynamics to hydrogen atoms?`langevinHydrogen`**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.PDB file containing Langevin parameters`langevinFile`**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.column of PDB from which to read coefficients`langevinCol`**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.

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* [14].

perform temperature coupling?`tCouple`**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.temperature for heat bath (K)`tCoupleTemp`**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.PDB file with tCouple parameters`tCoupleFile`**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.column of PDB from which to read coefficients`tCoupleCol`**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.

The stochastic velocity rescaling method originated by [15] can be viewed as an extension (and correction) of the Berendsen method. The implementation in NAMD is based on that from GROMACS, with some slight performance modifications during random number generation.

perform stochastic rescaling?`stochRescale`**Acceptable Values:**`on`or`off`**Default Value:**`off`**Description:**Specifies whether or not stochastic rescaling is active. If set to`on`, then the parameters`stochRescaleTemp`and`stochRescalePeriod`must be set.temperature for heat bath (K)`stochRescaleTemp`**Acceptable Values:**positive decimal**Description:**Temperature to which all atoms will be periodically readjusted toward. This temperature will be correctly maintained (in the canonical sense) over all atoms by rescaling the velocities with both deterministic (using the instantaneous temperature) and stochastic components.time parameter (ps) for temperature coupling`stochRescalePeriod`**Acceptable Values:**positive decimal**Description:**The stochastic rescaling algorithm holds for an arbitrary time parameter introduced when solving the Fokker-Planck equation. For systems predominantly composed of liquid water a value near 2 ps is appropriate and values between 0.5 and 2 ps are common in the literature for simulations of biomolecules. Larger values will generally result in weaker coupling and thus more NVE-like dynamics, but may also lead to slow (i.e. incorrect) convergence to the correct ensemble.number of timesteps between rescalings`stochRescaleFreq`**Acceptable Values:**positive integer**Default Value:**`stepsPerCycle`**Description:**The stochastic rescaling algorithm is invoked at fixed intervals. The effective time parameter is technically the ratio`stochRescaleFreq`/`stochRescalePeriod`(after converting into proper units using the value of`timestep`). The default should be adequate for most applications, but a smaller value closer to the frequency at which the nonbonded list is rebuilt would also be appropriate. When using multiple time stepping, it is important that rescaling occurs at timesteps that are integer multiples of the slowest interaction type (usually`fullElectFrequency`).Should heat transfer and work be computed?`stochRescaleHeat`**Acceptable Values:**`yes`or`no`**Default Value:**`no`**Description:**When active, the*cumulative*heat transfer with the thermostat will be reported as`HEAT`. The work due to the thermostat and integrator can then be computed as the change in total energy less the heat transfer and is reported as`WORK`. Note that the work includes all sources, including non-conservative elements of the Hamiltonian, but should otherwise approach zero for simulations at or near equilibrium. The accumulation starts at`firstTimestep`and can be reset from`Tcl`by re-setting this to zero.**This is an experimental option and not yet guaranteed for any specific purpose.**

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.

number of timesteps between temperature rescaling`rescaleFreq`**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.temperature for equilibration (K)`rescaleTemp`**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.

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.

number of timesteps between temperature reassignment`reassignFreq`**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.temperature for equilibration (K)`reassignTemp`**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.temperature increment for equilibration (K)`reassignIncr`**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.holding temperature for equilibration (K)`reassignHold`**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.

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 [53].

use Lowe-Andersen dynamics?`loweAndersen`**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.temperature for Lowe-Andersen calculations (K)`loweAndersenTemp`**Acceptable Values:**positive decimal**Description:**Temperature of the distribution used to set radial relative velocities. This determines the target temperature of the system.cutoff radius for Lowe-Andersen collisions (Å)`loweAndersenCutoff`**Acceptable Values:**positive decimal**Default Value:**2.7**Description:**Forces are only applied to atoms within this distance of one another.rate for Lowe-Andersen collisions (1/ps)`loweAndersenRate`**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.