NAMD configuration parameters

Input files

• coordinates $<$ coordinate PDB file $>$
  Acceptable Values: UNIX filename
  Description: The PDB file containing initial position coordinate data. Note that path names can be either absolute or relative. Only one value may be specified.

• structure $<$ PSF file $>$
  Acceptable Values: UNIX filename
  Description: The X-PLOR format PSF file describing the molecular system to be simulated. Only one value may be specified.

• parameters $<$ parameter file $>$
  Acceptable Values: UNIX filename
  Description: A CHARMM19, CHARMM22, or CHARMM27 parameter file that defines all or part of the parameters necessary for the molecular system to be simulated. At least one parameter file must be specified for each simulation. Multiple definitions (but only one file per definition) are allowed for systems that require more than one parameter file. The files will be read in the order that they appear in the configuration file. If duplicate parameters are read, a warning message is printed and the last parameter value read is used. Thus, the order that files are read can be important in cases where duplicate values appear in separate files.

• paraTypeXplor $<$ Is the parameter file in X-PLOR format? $>$
  Acceptable Values: on or off
  Default Value: on
  Description: Specifies whether or not the parameter file(s) are in X-PLOR format. X-PLOR format is the default for parameter files! Caveat: The PSF file should be also constructed with X-PLOR in case of an X-PLOR parameter file because X-PLOR stores information about the multiplicity of dihedrals in the PSF file. See the X-PLOR manual for details.

• paraTypeCharmm $<$ Is the parameter file in CHARMM format? $>$
  Acceptable Values: on or off
  Default Value: off
  Description: Specifies whether or not the parameter file(s) are in CHARMM format. X-PLOR format is the default for parameter files! Caveat: The information about multiplicity of dihedrals will be obtained directly from the parameter file, and the full multiplicity will be used (same behavior as in CHARMM). If the PSF file originates from X-PLOR, consecutive multiple entries for the same dihedral (indicating the dihedral multiplicity for X-PLOR) will be ignored.

• velocities $<$ velocity PDB file $>$
  Acceptable Values: UNIX filename
  Description: The PDB file containing the initial velocities for all atoms in the simulation. This is typically a restart file or final velocity file written by NAMD during a previous simulation. Either the temperature or the velocities/binvelocities option must be defined to determine an initial set of velocities. Both options cannot be used together.

• binvelocities $<$ binary velocity file $>$
  Acceptable Values: UNIX filename
  Description: The binary file containing initial velocities for all atoms in the simulation. A binary velocity file is created as output from NAMD by activating the binaryrestart or binaryoutput options. The binvelocities option should be used as an alternative to velocities. Either the temperature or the velocities/binvelocities option must be defined to determine an initial set of velocities. Both options cannot be used together.

• bincoordinates $<$ binary coordinate restart file $>$
  Acceptable Values: UNIX filename
  Description: The binary restart file containing initial position coordinate data. A binary coordinate restart file is created as output from NAMD by activating the binaryrestart or binaryoutput options. Note that, in the current implementation at least, the bincoordinates option must be used in addition to the coordinates option, but the positions specified by coordinates will then be ignored.

• cwd $<$ default directory $>$
  Acceptable Values: UNIX directory name
  Description: The default directory for input and output files. If a value is given, all filenames that do not begin with a / are assumed to be in this directory. For example, if cwd is set to /scr, then a filename of outfile would be modified to /scr/outfile while a filename of /tmp/outfile would remain unchanged. If no value for cwd is specified, than all filenames are left unchanged but are assumed to be relative to the directory which contains the configuration file given on the command line.

Output files

• outputname $<$ output file prefix $>$
  Acceptable Values: UNIX filename prefix
  Description: At the end of every simulation, NAMD writes two files, one containing the final coordinates and another containing the final velocities of all atoms in the simulation. This option specifies the file prefix for these two files as well as the default prefix for trajectory and restart files. The position coordinates will be saved to a file named as this prefix with .coor appended. The velocities will be saved to a file named as this prefix with .vel appended. For example, if the prefix specified using this option was /tmp/output, then the two files would be /tmp/output.coor and /tmp/output.vel.

• binaryoutput $<$ use binary output files? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: Enables the use of binary output files. If this option is not set to no, then the final output files will be written in binary rather than PDB format. Binary files preserve more accuracy between NAMD restarts than ASCII PDB files, but the binary files are not guaranteed to be transportable between computer architectures. (The atom count record is used to detect wrong-endian files, which works for most atom counts. The utility program flipbinpdb is provided to reformat these files if necessary.)

• restartname $<$ restart files prefix $>$
  Acceptable Values: UNIX filename prefix
  Default Value: outputname.restart
  Description: The prefix to use for restart filenames. NAMD produces restart files that store the current positions and velocities of all atoms at some step of the simulation. This option specifies the prefix to use for restart files in the same way that outputname specifies a filename prefix for the final positions and velocities. If restartname is defined then the parameter restartfreq must also be defined.

• restartfreq $<$ frequency of restart file generation $>$
  Acceptable Values: positive integer
  Description: The number of timesteps between the generation of restart files.

• restartsave $<$ use timestep in restart filenames? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Appends the current timestep to the restart filename prefix, producing a sequence of restart files rather than only the last version written.

• binaryrestart $<$ use binary restart files? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: Enables the use of binary restart files. If this option is not set to no, then the restart files will be written in binary rather than PDB format. Binary files preserve more accuracy between NAMD restarts than ASCII PDB files, but the binary files are not guaranteed to be transportable between computer architectures. (The atom count record is used to detect wrong-endian files, which works for most atom counts. The utility program flipbinpdb is provided to reformat these files if necessary.)

• DCDfile $<$ coordinate trajectory output file $>$
  Acceptable Values: UNIX filename
  Default Value: outputname.dcd
  Description: The binary DCD position coordinate trajectory filename. This file stores the trajectory of all atom position coordinates using the same format (binary DCD) as X-PLOR. If DCDfile is defined, then DCDfreq must also be defined.

• DCDfreq $<$ timesteps between writing coordinates to trajectory file $>$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of position coordinates to the trajectory file. The initial positions will not be included in the trajectory file. Positions in DCD files are stored in Å.

• DCDUnitCell $<$ write unit cell data to dcd file? $>$
  Acceptable Values: yes or no
  Default Value: yes if periodic cell
  Description: If this option is set to yes, then DCD files will contain unit cell information in the style of Charmm DCD files. By default this option is enabled if the simulation cell is periodic in all three dimensions and disabled otherwise.

• velDCDfile $<$ velocity trajectory output file $>$
  Acceptable Values: UNIX filename
  Default Value: outputname.veldcd
  Description: The binary DCD velocity trajectory filename. This file stores the trajectory of all atom velocities using the same format (binary DCD) as X-PLOR. If velDCDfile is defined, then velDCDfreq must also be defined.

• velDCDfreq $<$ timesteps between writing velocities to trajectory file $>$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of velocities to the trajectory file. The initial velocities will not be included in the trajectory file. Velocities in DCD files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR=20.45482706 to convert to Å/ps.

• forceDCDfile $<$ force trajectory output file $>$
  Acceptable Values: UNIX filename
  Default Value: outputname.forcedcd
  Description: The binary DCD force trajectory filename. This file stores the trajectory of all atom forces using the same format (binary DCD) as X-PLOR. If forceDCDfile is defined, then forceDCDfreq must also be defined.

• forceDCDfreq $<$ timesteps between writing force to trajectory file $>$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of forces to the trajectory file. The initial forces will not be included in the trajectory file. Forces in DCD files are stored in kcal/mol/Å. In the current implementation only those forces that are evaluated during the timestep that a frame is written are included in that frame. This is different from the behavior of TclForces and is likely to change based on user feedback. For this reason it is strongly recommended that forceDCDfreq be a multiple of fullElectFrequency.

Standard output

NAMD logs a variety of summary information to standard output. The standard units used by NAMD are Angstroms for length, kcal/mol for energy, Kelvin for temperature, and bar for pressure. Wallclock or CPU times are given in seconds unless otherwise noted.

BOUNDARY energy is from spherical boundary conditions and harmonic restraints, while MISC energy is from external electric fields and various steering forces. TOTAL is the sum of the various potential energies, and the KINETIC energy. TOTAL2 uses a slightly different kinetic energy that is better conserved during equilibration in a constant energy ensemble. Although TOTAL2 is calculated internally for producing TOTAL3, its value is no longer output during simulation. TOTAL3 is another variation with much smaller short-time fluctuations that is also adjusted to have the same running average as TOTAL2. Defects in constant energy simulations are much easier to spot in TOTAL3 than in TOTAL or TOTAL2.

PRESSURE is the pressure calculated based on individual atoms, while GPRESSURE incorporates hydrogen atoms into the heavier atoms to which they are bonded, producing smaller fluctuations. The TEMPAVG, PRESSAVG, and GPRESSAVG are the average of temperature and pressure values since the previous ENERGY output; for the first step in the simulation they will be identical to TEMP, PRESSURE, and GPRESSURE.

Performance for NAMD's new GPU-resident mode is improved by avoiding calculation of energy and virial reductions except when needed. This means that the averages are no longer calculated over all values since the previous ENERGY output. Instead, a moving average is calculated over the previously output values, using a fixed window size defined by a config file parameter. GPU-resident mode replaces TOTAL3 with TOTALAVG, a moving average over the previous TOTAL energy values.

• outputEnergies $<$ timesteps between energy output $>$
  Acceptable Values: positive integer
  Default Value: 1
  Description: The number of timesteps between each energy output of NAMD. This value specifies how often NAMD should output the current energy values to stdout (which can be redirected to a file). By default, this is done every step. For long simulations, the amount of output generated by NAMD can be greatly reduced by outputting the energies only occasionally. For GPU-resident mode, the default value is raised to 100, although performance might be improved by setting it higher.

• movingAverageWindowSize $<$ fixed window size for calculating moving averages $>$
  Acceptable Values: positive integer
  Default Value: 20
  Description: In GPU-resident mode, the energy, temperature, and pressure averages are calculated as moving averages over the previously outputted values. Changing the window size does not affect performance.

• computeEnergies $<$ timesteps between energy evaluation $>$
  Acceptable Values: positive integer
  Default Value: outputEnergies
  Description: The number of timesteps between each energy evaluation of NAMD. This value specifies how often NAMD should compute the current energy values. The default value is to keep the same as outputEnergies. Other operations requiring the energies, involving outputEnergies, alchOutFreq and the period of calling a callback TCL procedure, should be a multiple of this value. In the GPU build of NAMD, increasing the value of this option can improve the performance since the evaluation of energies requires double-precision mathematical operations.

• outputEnergiesPrecision $<$ energy output precision $>$
  Acceptable Values: positive integer
  Default Value: 4
  Description: The number of decimal digits used when printing NAMD energies. Increasing the output precision will skew the aligned 80-column format that NAMD has traditionally provided. To keep energy output aligned, increase the terminal width by 5 columns for each additional decimal digit beyond 4.

• mergeCrossterms $<$ add crossterm energy to dihedral? $>$
  Acceptable Values: yes or no
  Default Value: yes
  Description: If crossterm (or CMAP) terms are present in the potential, the energy is added to the dihedral energy to avoid altering the energy output format. Disable this feature to add a separate ``CROSS'' field to the output.

• outputMomenta $<$ timesteps between momentum output $>$
  Acceptable Values: nonnegative integer
  Default Value: 0
  Description: The number of timesteps between each momentum output of NAMD. If specified and nonzero, linear and angular momenta will be output to stdout.

• outputPressure $<$ timesteps between pressure output $>$
  Acceptable Values: nonnegative integer
  Default Value: 0
  Description: The number of timesteps between each pressure output of NAMD. If specified and nonzero, atomic and group pressure tensors will be output to stdout.

• outputTiming $<$ timesteps between timing output $>$
  Acceptable Values: nonnegative integer
  Default Value: the greater of firstLdbStep or $10 \times$ outputEnergies
  Description: The number of timesteps between each timing output of NAMD. If nonzero, CPU and wallclock times and memory usage will be output to stdout. These data are from node 0 only; CPU times and memory usage for other nodes may vary.

• outputPerformance $<$ Print performance statistics? $>$
  Acceptable Values: ``on'' or ``off''
  Default Value: on
  Description: When enabled, every ``TIMING:'' line is immediately followed by a ``PERFORMANCE:'' line that states the average ns/day performance.

Output Selection

For the cases when it is preferable to have trajectory output of a subset of the atoms, selections can be defined and assigned independent output frequencies and output file names.

Atom selections are defined by creating a PDB file where the temperaturefactor field (AKA beta in VMD) is assigned a value greater than zero for each atom in the selection. For example, when the objective is to have a more frequent output trajectory containing no solvent, the following VMD commands will produce an appropriate selection PDB.

(Note: example assumes structure and coordinates are already loaded)

set allatoms [atomselect top "all"]
set soluteatoms [atomselect top "not water and not ions"]
$allatoms set beta 0
$soluteatoms set beta 1
$allatoms writepdb solute.pdb
$soluteatoms writepsf solute.psf

The additional PSF file in the prior example is not necessary for NAMD, but would be useful in VMD, or other subsequent analysis, to examine the trajectory associated with given selection of atoms.

Such selections can be used within NAMD using the arguments described below. A maximum of $16$ such selections is allowed. There are no restrictions regarding atoms belonging to multiple selections. Each selection is identified by a user defined string tag to bind the frequency and input file and output file definitions together for each selection. The tag is an alphanumeric string without spaces, up to $80$ characters in length, which identifies to which selection the specified field applies.

• DcdSelection $<$ enable user defined output? $>$
  Acceptable Values: yes or no
  Default Value: no
  Description: Specifies whether or not any user defined selections are being used.

• DcdSelectionInputfile $<$ tag $>$ $<$ user selection PDB input file $>$
  Acceptable Values: UNIX filename
  Default Value: inputfilename.pdb
  Description: The PDB file containing a record for each atom in the system with the beta field set greater than zero for the atoms in the user selection and left zero for the atoms output the user selection. If DcdSelectionInputfile is defined, then DcdSelectionfile and DcdSelectionfreq must also be defined.

• DcdSelectionfile $<$ tag $>$ $<$ user selection coordinate trajectory output file $>$
  Acceptable Values: UNIX filename
  Default Value: outputname.dcd
  Description: The binary DCD position coordinate trajectory filename for the user selection. This file stores the trajectory of all atom position coordinates using the same format (binary DCD) as X-PLOR. If DcdSelectionfile is defined, then DcdSelectionfreq must also be defined.

• DcdSelectionfreq $<$ tag $>$ $<$ timesteps between writing coordinates to user selection trajectory file $>$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of position coordinates to the trajectory file. The initial positions will not be included in the trajectory file. Positions in DCD files are stored in Å.

In the case of the example above, the following configuration would be valid:

dcdSelection yes
dcdSelectionInputfile soluteonly solute.pdb
dcdSelectionfreq soluteonly 100
dcdSelectionfile soluteonly solute.dcd

NOTE: This feature is not currently compatible with special memory-optimized NAMD builds https://www.ks.uiuc.edu/Research/namd/wiki/index.cgi?NamdMemoryReduction.

See lib/replica/examples/mplexjob0-dcdselect.conf for replica usage.