NAMD Examples

Blacklight

This job is a 1 ps simulation of decalanin (66 atoms) with a CHARMM force field at 300° K.

• namd.pbs, the script file.
• alanin.namd, the configuration file.
• alanin.pdb, the coordinates file (input)
• alanin.psf, the structure file (input)
• alanin.params, the parameter file (input)
• alanin.coor, coordinates file (output)
• alanin.vel, velocity file (output)
• alanin.xsc, system config file (output)
• alanin.log, output from the namd run
• alanin.out, stdout and stderr from the job

Salk

This job is a 1 ps simulation of decalanin (66 atoms) with a CHARMM force field at 300° K.

• namd.pbs, the script file.
• alanin.namd, the configuration file.
• alanin.pdb, the coordinates file (input)
• alanin.psf, the structure file (input)
• alanin.params, the parameter file (input)
• alanin.coor, coordinates file (output)
• alanin.vel, velocity file (output)
• alanin.xsc, system config file (output)
• alanin.log, output from the namd run
• alanin.out, stdout and stderr from the job

Warhol job

This job is a 1 ps simulation of decalanin (66 atoms) with a CHARMM force field at 300° K.

• namd.pbs, the script file.
• alanin.namd, the configuration file.
• alanin.pdb, the coordinates file (input)
• alanin.psf, the structure file (input)
• alanin.params, the parameter file (input)
• alanin.coor, coordinates file (output)
• alanin.vel, velocity file (output)
• alanin.xsc, system config file (output)
• alanin.log, output from the namd run
• alanin.out, stdout and stderr from the job