Input files

• coordinates $\langle$ coordinate PDB file $\rangle$
  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 $\langle$ PSF file $\rangle$
  Acceptable Values: UNIX filename
  Description:  The X-PLOR style PSF file describing the molecular system to be simulated. Only one value may be specified.

• parameters $\langle$ parameter file $\rangle$
  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.

• velocities $\langle$ velocity PDB file $\rangle$
  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 $\langle$ binary velocity file $\rangle$
  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 option. 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 $\langle$ binary coordinate restart file $\rangle$
  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 option. 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 $\langle$ default directory $\rangle$
  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.