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 or CHARMM22 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 are allowed for systems that require more than one parameter file. For example, if three files were needed, lines such as:

  
  

  parameters param1

  parameters param2

  parameters param3

  
  

  could be added to the configuration 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 PDB file $>$
  Acceptable Values: UNIX filename prefix
  Description: At the end of every simulation, NAMD writes two PDB 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. 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: Activates the use of binary output files. If this option is set to yes, 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 utility program flipbinpdb is provided with the Linux/Intel version to reformat these files.)

• restartname $<$ restart files $>$
  Acceptable Values: UNIX filename prefix
  Description: The prefix to use for restart filenames. NAMD produces PDB 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. If restartfreq is defined, then restartname must also be defined.

• 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: Activates the use of binary restart files. If this option is set to yes, 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 utility program flipbinpdb is provided with the Linux/Intel version to reformat these files.)

• DCDfile $<$ coordinate trajectory output file $>$
  Acceptable Values: UNIX filename
  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 be included in the trajectory file unless the firsttimestep parameter is set non-zero.

• velDCDfile $<$ velocity trajectory output file $>$
  Acceptable Values: UNIX filename
  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 be included in the trajectory file unless the firsttimestep parameter is set non-zero.

• 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.

• 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: 0
  Description: The number of timesteps between each timing output of NAMD. If specified and nonzero, CPU and wallclock times will be output to stdout. These data are from node 0 only; CPU times for other nodes may vary.