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Subsections


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 [14], although a different integrator is used.

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 [14].

Stochastic velocity rescaling parameters

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.

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.

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.

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 [56].


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Next: Pressure Control Up: Standard Minimization and Dynamics Previous: Dynamics
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