VMD has been designed to operate from the command line. This allows files to be loaded directly at start up. The commands to load a prmtop file and an inpcrd file that have just been generated would be:
$ vmd -parm7 name_of_file.prmtop -rst7 name_of_file.inpcrd
The -parm7 flag signifies an AMBER7 prmtop and the -rst7 flag signifies an
AMBER7 restart file.
Don’t let the AMBER7 scare you–AMBER switched formats for prmtops and restarts
several years ago, and the name stuck around to mean anything file generated
with or after AMBER7.
If you wanted to look at a trajectory that has not had ioutfm explicitly set
to 0 in the mdin files when working with AMBER16 (or later), then you would use:
$ vmd -parm7 name_of_file_wat.prmtop -netcdf name_of_file_wat_md25.mdcrd
or
for a restart file which has not had ntxo explicitly set to 1 in the mdin files
$ vmd -parm7 name_of_file_wat.prmtop -netcdf name_of_solvated_file_wat_md.rst
The rst file extension is just the last saved trajectory, and the mdcrd
file extension contains all of the trajectory information for that segment
(whose time frame changes based on the input settings).
NetCDF is a condensed standardized format, and is really what these files have
been saved as because that is the default, starting with AMBER16.
Previous editions of AMBER wrote the mdcrd and rst files in ASCII format,
and the flag to read those in would be -crd.
PDBs can be loaded with the the -pdb flag.