File formats

PDB files

The PDB (Protein Data Bank) format is used for coordinate, velocity, force, or other data being read or written by NAMD. This is the standard format for coordinate data for most other molecular dynamics programs as well, including X-PLOR and CHARMM. A full description of this file format can be obtained from the PDB web site at http://www.rcsb.org/pdb/. Positions in PDB files are stored in Å. Velocities in PDB files are stored in Å/ps and may be divided by PDBVELFACTOR=20.45482706 to convert to the NAMD internal units used in DCD and NAMD binary files. Forces in PDB files are stored in kcal/mol/Å. NAMD binary files (below) should be preferred to PDB files in most cases due to their higher precision.

X-PLOR format PSF files

NAMD uses the same protein structure files that X-PLOR does. These files may be generated with psfgen, VMD, X-PLOR, or CHARMM. CHARMM can generate an X-PLOR format PSF file with the command ``write psf card xplor''.

CHARMM19, CHARMM22, and CHARMM27 parameter files

NAMD supports CHARMM19, CHARMM22, and CHARMM27 parameter files in both X-PLOR and CHARMM formats. (X-PLOR format is the default, CHARMM format parameter files may be used given the parameter ``paraTypeCharmm on''.) For a full description of the format of commands used in these files, see the X-PLOR and CHARMM User's Manual [12].

DCD trajectory files

NAMD produces DCD trajectory files in the same format as X-PLOR and CHARMM. The DCD files are single precision binary FORTRAN files, so are transportable between computer architectures. The file readers in NAMD and VMD can detect and adapt to the endianness of the machine on which the DCD file was written, and the utility program flipdcd is also provided to reformat these files if needed. The exact format of these files is very ugly but supported by a wide range of analysis and display programs. The timestep is stored in the DCD file in NAMD internal units and must be multiplied by TIMEFACTOR=48.88821 to convert to fs. Positions in DCD files are stored in Å. Velocities in DCD files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR=20.45482706 to convert to Å/ps. Forces in DCD files are stored in kcal/mol/Å.

NAMD binary files

NAMD uses a trivial double-precision binary file format for coordinates, velocities, and forces. Due to its high precision this is the default output and restart format. VMD refers to these files as the ``namdbin'' format. The file consists of the atom count as a 32-bit integer followed by all three position or velocity components for each atom as 64-bit double-precision floating point, i.e., NXYZXYZXYZXYZ... where N is a 4-byte int and X, Y, and Z are 8-byte doubles. If the number of atoms the file contains is known then the atom count can be used to determine endianness. The file readers in NAMD and VMD can detect and adapt to the endianness of the machine on which the binary file was written, and the utility program flipbinpdb is also provided to reformat these files if needed. Positions in NAMD binary files are stored in Å. Velocities in NAMD binary files are stored in NAMD internal units and must be multiplied by PDBVELFACTOR=20.45482706 to convert to Å/ps. Forces in NAMD binary files are stored in kcal/mol/Å.