NAME¶

gmx - master command for GROMACS suite

SYNOPSIS¶

gmx [ options ] command [ command options ... ]

DESCRIPTION¶

gmx is the unified interface for nearly all GROMACS operations. For a list of all available commands, run gmx help command , and for detailed help on a specific command, e.g. rms, run gmx help rms or read the (equivalent) man page for gmx-rms(1).

SELECTION SYNTAX AND USAGE¶

Selections are used to select atoms/molecules/residues for analysis. In contrast to traditional index files, selections can be dynamic, i.e., select different atoms for different trajectory frames. Each analysis tool requires a different number of selections and the selections are interpreted differently. The general idea is still the same: each selection evaluates to a set of positions, where a position can be an atom position or center-of-mass or center-of-geometry of a set of atoms. The tool then uses these positions for its analysis to allow very flexible processing. Some analysis tools may have limitations on the types of selections allowed. To get started with selections, run, e.g., gmx select without specifying selections on the command-line and use the interactive prompt to try out different selections. This tool provides output options that allow one to see what is actually selected by the given selections, and the interactive prompt reports syntax errors immediately, allowing one to try again. The subtopics listed below give more details on different aspects of selections. Available subtopics:

arithmetic Arithmetic expressions in selections

cmdline Specifying selections from command line

evaluation Selection evaluation and optimization

examples Selection examples

keywords Selection keywords

limitations Selection limitations

positions Specifying positions in selections

syntax Selection syntax

View these selections with gmx help selection SUBTOPIC.

GLOBAL OPTIONS¶

For command specific options, see gmx help COMMAND.

-h

Print help and quit.

-quiet

Do not print common startup info or quotes.

-version

Print extended version information and quit.

-copyright

Print copyright information on startup.

All of these options can be suppressed by a leading "no", e.g. -noquiet.

SEE ALSO¶

/usr/share/doc/gromacs