Translation between NAMD and X-PLOR configuration parameters

NAMD was designed to provide many of the same molecular dynamics functions that X-PLOR provides. As such, there are many similarities between the types of parameters that must be passed to both X-PLOR and NAMD. This section describes relations between similar NAMD and X-PLOR parameters.

• NAMD Parameter: cutoff
  X-PLOR Parameter: CTOFNB
  When full electrostatics are not in use within NAMD, these parameters have exactly the same meaning -- the distance at which electrostatic and van der Waals forces are truncated. When full electrostatics are in use within NAMD, the meaning is still very similar. The van der Waals force is still truncated at the specified distance, and the electrostatic force is still computed at every timestep for interactions within the specified distance. However, the NAMD integration uses multiple time stepping to compute electrostatic force interactions beyond this distance every stepspercycle timesteps.

• NAMD Parameter: vdwswitchdist
  X-PLOR Parameter: CTONNB
  Distance at which the van der Waals switching function becomes active.

• NAMD Parameter: pairlistdist
  X-PLOR Parameter: CUTNb
  Distance within which interaction pairs will be included in pairlist.

• NAMD Parameter: 1-4scaling
  X-PLOR Parameter: E14Fac
  Scaling factor for 1-4 pair electrostatic interactions.

• NAMD Parameter: dielectric
  X-PLOR Parameter: EPS
  Dielectric constant.

• NAMD Parameter: exclude
  X-PLOR Parameter: NBXMod
  Both parameters specify which atom pairs to exclude from non-bonded interactions. The ability to ignore explicit exclusions is not present within NAMD, thus only positive values of NBXMod have NAMD equivalents. These equivalences are
  • NBXMod=1 is equivalent to exclude=none -- no atom pairs excluded,
  • NBXMod=2 is equivalent to exclude=1-2 -- only 1-2 pairs excluded,
  • NBXMod=3 is equivalent to exclude=1-3 -- 1-2 and 1-3 pairs excluded,
  • NBXMod=4 is equivalent to exclude=1-4 -- 1-2, 1-3, and 1-4 pairs excluded,
  • NBXMod=5 is equivalent to exclude=scaled1-4 -- 1-2 and 1-3 pairs excluded, 1-4 pairs modified.

• NAMD Parameter: switching
  X-PLOR Parameter: SHIFt, VSWItch, and TRUNcation
  Activating the NAMD option switching is equivalent to using the X-PLOR options SHIFt and VSWItch. Deactivating switching is equivalent to using the X-PLOR option TRUNcation.

• NAMD Parameter: temperature
  X-PLOR Parameter: FIRSttemp
  Initial temperature for the system.

• NAMD Parameter: rescaleFreq
  X-PLOR Parameter: IEQFrq
  Number of timesteps between velocity rescaling.

• NAMD Parameter: rescaleTemp
  X-PLOR Parameter: FINAltemp
  Temperature to which velocities are rescaled.

• NAMD Parameter: restartname
  X-PLOR Parameter: SAVE
  Filename prefix for the restart files.

• NAMD Parameter: restartfreq
  X-PLOR Parameter: ISVFrq
  Number of timesteps between the generation of restart files.

• NAMD Parameter: DCDfile
  X-PLOR Parameter: TRAJectory
  Filename for the position trajectory file.

• NAMD Parameter: DCDfreq
  X-PLOR Parameter: NSAVC
  Number of timesteps between writing coordinates to the trajectory file.

• NAMD Parameter: velDCDfile
  X-PLOR Parameter: VELOcity
  Filename for the velocity trajectory file.

• NAMD Parameter: velDCDfreq
  X-PLOR Parameter: NSAVV
  Number of timesteps between writing velocities to the trajectory file.

• NAMD Parameter: numsteps
  X-PLOR Parameter: NSTEp
  Number of simulation timesteps to perform.