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.

• useConstantArea $<$ constant area and normal pressure conditions $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: When enabled, NAMD keeps the dimension of the unit cell in the x-y plane constant while allowing fluctuations along the z axis. 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.

• SurfaceTensionTarget $<$ Surface tension target (dyn/cm) $>$
  Acceptable Values: decimal
  Default Value: 0.0
  Description: Specifies surface tension target. Must be used with useFlexibleCell and periodic boundary conditions. The pressure specified in LangevinPistonTarget becomes the pressure along the z axis, and surface tension is applied in the x-y plane.

• 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.

• ExcludeFromPressure $<$ Should some atoms be excluded from pressure rescaling? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not to exclude some atoms from pressure rescaling. The coordinates and velocites of such atoms are not rescaled during constant pressure simulations, though they do contribute to the virial calculation. May be useful for membrane protein simulation. EXPERIMENTAL.

• ExcludeFromPressureFile $<$ File specifying excluded atoms $>$
  Acceptable Values: PDB file
  Default Value: coordinates file
  Description: PDB file with one column specifying which atoms to exclude from pressure rescaling. Specify 1 for excluded and 0 for not excluded.

• ExcludeFromPressureCol $<$ Column in PDB file for specifying excluded atoms $>$
  Acceptable Values: O, B, X, Y, or Z
  Default Value: O
  Description: Specifies which column of the pdb file to check for excluded atoms.