Options

• Optional files are not used unless the option is set, in contrast to non optional files, where the default file name is used when the option is not set.

  All GROMACS programs will accept file options without a file extension or filename being specified. In such cases the default filenames will be used. With multiple input file types, such as generic structure format, the directory will be searched for files of each type with the supplied or default name. When no such file is found, or with output files the first file type will be used.

  All GROMACS programs with the exception of mdrun, trjcat and eneconv check if the command line options are valid. If this is not the case, the program will be halted.

• All GROMACS programs have 4 hidden options:

  option	type	default	description
  -[no]hidden	bool	yes	[hidden] Print hidden options
  -[no]quiet	bool	no	[hidden] Do not print help info
  -man	enum	html	[hidden] Write manual and quit: no, html, tex, nroff, java, ascii or completion
  -[no]debug	bool	no	[hidden] Write file with debug information

• Enumerated options (enum) should be used with one of the arguments listed in the option description, the argument may be abbreviated. The first match to the shortest argument in the list will be selected.

• Vector options can be used with 1 or 3 parameters. When only one parameter is supplied the two others are also set to this value.

• All GROMACS programs can read compressed or g-zipped files. There might be a problem with reading compressed .xtc, .trr and .trj files, but these will not compress very well anyway.

• Most GROMACS programs can process a trajectory with less atoms than the run input or structure file, but only if the trajectory consists of the first n atoms of the run input or structure file.