Pressure Control

The following options affect all pressure control methods.

• useGroupPressure $<$ group or atomic quantities $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Pressure can be calculated using either the atomic virial and kinetic energy (the default) or a hydrogen-group based pseudo-molecular virial and kinetic energy. The latter fluctuates less and is required in conjunction with rigidBonds (SHAKE).

• useFlexibleCell $<$ anisotropic cell fluctuations $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: NAMD allows the three orthogonal dimensions of the periodic cell to fluctuate independently when this option is enabled. This is not currently implemented in Berendsen's method.

Berendsen pressure bath coupling

NAMD provides constant pressure simulation using Berendsen's method. The following parameters are used to define the algorithm.

• BerendsenPressure $<$ use Berendsen pressure bath coupling? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not Berendsen pressure bath coupling is active. If set to on, then the parameters BerendsenPressureTarget, BerendsenPressureCompressibility and BerendsenPressureRelaxationTime must be set and the parameter BerendsenPressureFreq can optionally be set to control the behavior of this feature.

• BerendsenPressureTarget $<$ target pressure (bar) $>$
  Acceptable Values: positive decimal
  Description: Specifies target pressure for Berendsen's method.

• BerendsenPressureCompressibility $<$ compressibility (bar$^{-1}$) $>$
  Acceptable Values: positive decimal
  Description: Specifies compressibility for Berendsen's method.

• BerendsenPressureRelaxationTime $<$ relaxation time (fs) $>$
  Acceptable Values: positive decimal
  Description: Specifies relaxation time for Berendsen's method.

• BerendsenPressureFreq $<$ how often to rescale positions $>$
  Acceptable Values: positive multiple of nonbondedFrequency and fullElectFrequency
  Default Value: nonbondedFrequency or fullElectFrequency if used
  Description: Specifies number of timesteps between position rescalings for Berendsen's method.

Nosé-Hoover Langevin piston pressure control

NAMD provides constant pressure simulation using a modified Nosé-Hoover method in which Langevin dynamics is used to control fluctuations in the barostat. This method should be combined with a method of temperature control, such as Langevin dynamics, in order to simulate the NPT ensemble. The following parameters are used to define the algorithm.

• LangevinPiston $<$ use Langevin piston pressure control? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not Langevin piston pressure control is active. If set to on, then the parameters LangevinPistonTarget, LangevinPistonPeriod, LangevinPistonDecay and LangevinPistonTemp must be set.

• LangevinPistonTarget $<$ target pressure (bar) $>$
  Acceptable Values: positive decimal
  Description: Specifies target pressure for Langevin piston method.

• LangevinPistonPeriod $<$ oscillation period (fs) $>$
  Acceptable Values: positive decimal
  Description: Specifies barostat oscillation time scale for Langevin piston method.

• LangevinPistonDecay $<$ damping time scale (fs) $>$
  Acceptable Values: positive decimal
  Description: Specifies barostat damping time scale for Langevin piston method.

• LangevinPistonTemp $<$ noise temperature (K) $>$
  Acceptable Values: positive decimal
  Description: Specifies barostat noise temperature for Langevin piston method. This should be set equal to the target temperature for the chosen method of temperature control.

• StrainRate $<$ initial strain rate $>$
  Acceptable Values: decimal triple (x y z)
  Default Value: 0. 0. 0.
  Description: Optionally specifies the initial strain rate for pressure control. Is overridden by value read from file specified with extendedSystem.