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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.
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