Output files

• outputname $\langle$ output PDB file $\rangle$
  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.

• restartname $\langle$ restart files $\rangle$
  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 $\langle$ frequency of restart file generation $\rangle$
  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.

• binaryrestart $\langle$ use binary restart files? $\rangle$
  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 and 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.

• DCDfile $\langle$ coordinate trajectory output file $\rangle$
  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 $\langle$ timesteps between writing coordinates to trajectory file $\rangle$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of position coordinates to the trajectory file.

• velDCDfile $\langle$ velocity trajectory output file $\rangle$
  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 $\langle$ timesteps between writing velocities to trajectory file $\rangle$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of velocities to the trajectory file.

• electForceDCDfile $\langle$ electrostatic force trajectory file $\rangle$
  Acceptable Values: UNIX filename prefix
  Description: The binary DCD short and long range electrostatic force trajectory filename prefix. The short and long range electrostatic force trajectories will be respectively stored in files with .s and .l appended to this prefix. If electForceDCDfile is defined, then electForceDCDfreq must also be defined.

• electForceDCDfreq $\langle$ timesteps between writing electrostatic forces to trajectory file $\rangle$
  Acceptable Values: positive integer
  Description: The number of timesteps between writing to the long and short range electrostatic force trajectory files.

• allForceDCDfile $\langle$ total force trajectory file $\rangle$
  Acceptable Values: UNIX filename
  Description: The binary DCD total force trajectory filename. This file stores the trajectory of the total forces on each atom. If allForceDCDfile is defined, then allForceDCDfreq must also be defined.

• allForceDCDfreq $\langle$ timesteps between writing total forces to trajectory file $\rangle$
  Acceptable Values: positive integer
  Description: The number of timesteps between the writing of total forces to the trajectory file.

• outputEnergies $\langle$ timesteps between energy output $\rangle$
  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.