PDB files contains data about atoms, residues, segment names, occupancy and beta factor, and one coordinate set. PSF and PARM files contain atoms, residues, segment names, residue types, atomic mass and charge, and the bond connectivity. VMD supports four file formats used by Gromacs: GRO, G96, TRR and XTC. GRO and G96 files contain structure information including atoms, residue and segment data, and one coordinate set. CRD, DCD, TRR and XTC files contain only coordinate data (frames ). It should be noted that while PDB, GRO and G96 files were designed to contain only one coordinate set, multiple files can be concatenated into one larger file to create a makeshift trajectory file which can be loaded by VMD.
When VMD loads a file it requires information about atom names and coordinates and tries to fill in the rest. Since the PDB file contains all this information, it does not need to be loaded with any other data files. However, the PDB file doesn't contain the atom types, masses, and charges, so these are guessed or assigned default values. In particular, charges will be assigned a value of 0.0 if the file does not contain explicit charge information.
A PSF file does not contain coordinate information so it must be loaded along with a PDB or DCD file. If a PDB and PSF are given there is no missing data and VMD makes no assumptions. If a PSF and DCD are given then only the chain identifier and occupancy and beta values are missing so they are given a default value. A PARM file is similar to a PSF in that it too contains no coordinate information. It must be loaded along with a CRD trajectory file. If a PARM and CRD file are loaded together, then only the segname and chain ID for the atoms are left blank. A CRD or DCD file can be specified along with the PDB, in which case the PDB file will be read as normal, and then coordinate sets are read from the DCD or CRD until the end of the file is reached. Gromacs GRO and G96 files can be loaded on their own since they contain the necessary atom data and coordinates. They can also be loaded along with TRR and XTC files to obtain trajectory data. Additional coordinates from a PDB, CRD, or DCD file can be appended to the current coordinate set using the Molecule File Browser form.