Command-line reference ====================== .. toctree:: :hidden: :glob: /onlinehelp/gmx /onlinehelp/gmx-* |Gromacs| includes many tools for preparing, running and analysing molecular dynamics simulations. These are all structured as part of a single :command:`gmx` wrapper binary, and invoked with commands like :command:`gmx grompp`. :ref:`mdrun ` is the only other binary that :ref:`can be built `; in the normal build it can be run with :command:`gmx mdrun`. Documentation for these can be found at the respective sections below, as well as on man pages (e.g., :manpage:`gmx-grompp(1)`) and with :samp:`gmx help {command}` or :samp:`gmx {command} -h`. If you've installed an MPI version of |Gromacs|, by default the :command:`gmx` binary is called :command:`gmx_mpi` and you should adapt accordingly. Command-line interface and conventions -------------------------------------- All |Gromacs| commands require an option before any arguments (i.e., all command-line arguments need to be preceded by an argument starting with a dash, and values not starting with a dash are arguments to the preceding option). Most options, except for boolean flags, expect an argument (or multiple in some cases) after the option name. The argument must be a separate command-line argument, i.e., separated by space, as in ``-f traj.xtc``. If more than one argument needs to be given to an option, they should be similarly separated from each other. Some options also have default arguments, i.e., just specifying the option without any argument uses the default argument. If an option is not specified at all, a default value is used; in the case of optional files, the default might be not to use that file (see below). All |Gromacs| command options start with a single dash, whether they are single- or multiple-letter options. However, two dashes are also recognized (starting from 5.1). In addition to command-specific options, some options are handled by the :command:`gmx` wrapper, and can be specified for any command. See :doc:`wrapper binary help ` for the list of such options. These options are recognized both before the command name (e.g., :command:`gmx -quiet grompp`) as well as after the command name (e.g., :command:`gmx grompp -quiet`). There is also a ``-hidden`` option that can be specified in combination with ``-h`` to show help for advanced/developer-targeted options. Most analysis commands can process a trajectory with fewer 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. Handling specific types of command-line options ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ boolean options Boolean flags can be specified like ``-pbc`` and negated like ``-nopbc``. It is also possible to use an explicit value like ``-pbc no`` and ``-pbc yes``. file name options Options that accept files names have features that support using default file names (where the default file name is specific to that option): * If a required option is not set, the default is used. * If an option is marked optional, the file is not used unless the option is set (or other conditions make the file required). * If an option is set, and no file name is provided, the default is used. All such options will accept file names without a file extension. The extension is automatically appended in such a case. When multiple input formats are accepted, such as a generic structure format, the directory will be searched for files of each type with the supplied or default name. When no file with a recognized extension is found, an error is given. For output files with multiple formats, a default file type will be used. Some file formats can also be read from compressed (:file:`.Z` or :file:`.gz`) formats. enum options Enumerated options (enum) should be used with one of the arguments listed in the option description. The argument may be abbreviated, and the first match to the shortest argument in the list will be selected. vector options Some options accept a vector of values. Either 1 or 3 parameters can be supplied; when only one parameter is supplied the two other values are also set to this value. selection options See :doc:`/onlinehelp/selections`. Commands by name ---------------- .. include:: /fragments/byname.rst Commands by topic ----------------- .. include:: /fragments/bytopic.rst Special topics -------------- The information in these topics is also accessible through :samp:`gmx help {topic}` on the command line. Selection syntax and usage ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. toctree:: /onlinehelp/selections .. _command-changes: Command changes between versions -------------------------------- Starting from |Gromacs| 5.0, some of the analysis commands (and a few other commands as well) have changed significantly. One main driver for this has been that many new tools mentioned below now accept selections through one or more command-line options instead of prompting for a static index group. To take full advantage of selections, the interface to the commands has changed somewhat, and some previous command-line options are no longer present as the same effect can be achieved with suitable selections. Please see :doc:`/onlinehelp/selections` additional information on how to use selections. In the process, some old analysis commands have been removed in favor of more powerful functionality that is available through an alternative tool. For removed or replaced commands, this page documents how to perform the same tasks with new tools. For new commands, a brief note on the available features is given. See the linked help for the new commands for a full description. This section lists only major changes; minor changes like additional/removed options or bug fixes are not typically included. Version 5.1 ^^^^^^^^^^^ General ....... Symbolic links from 5.0 are no longer supported. The only way to invoke a command is through :samp:`gmx {}`. gmx pairdist ............ **new** :ref:`gmx pairdist` has been introduced as a selection-enabled replacement for :ref:`gmx mindist` (``gmx mindist`` still exists unchanged). It can calculate min/max pairwise distances between a pair of selections, including, e.g., per-residue minimum distances or distances from a single point to a set of residue-centers-of-mass. gmx rdf ....... **rewritten** :ref:`gmx rdf` has been rewritten for 5.1 to use selections for specifying the points from which the RDFs are calculated. The interface is mostly the same, except that there are new command-line options to specify the selections. The following additional changes have been made: * ``-com`` and ``-rdf`` options have been removed. Equivalent functionality is available through selections: * ``-com`` can be replaced with a :samp:`com of {}` as the reference selection. * ``-rdf`` can be replaced with a suitable set of selections (e.g., :samp:`res_com of {}`) and/or using ``-seltype``. * ``-rmax`` option is added to specify a cutoff for the RDFs. If set to a value that is significantly smaller than half the box size, it can speed up the calculation significantly if a grid-based neighborhood search can be used. * ``-hq`` and ``-fade`` options have been removed, as they are simply postprocessing steps on the raw numbers that can be easily done after the analysis. Version 5.0 ^^^^^^^^^^^ General ....... Version 5.0 introduced the :command:`gmx` wrapper binary. For backwards compatibility, this version still creates symbolic links by default for old tools: e.g., ``g_order `` is equivalent to ``gmx order ``, and ``g_order`` is simply a symbolic link on the file system. g_bond ...... **replaced** This tool has been removed in 5.0. A replacement is :ref:`gmx distance`. You can provide your existing index file to :ref:`gmx distance`, and it will calculate the same distances. The differences are: * ``-blen`` and ``-tol`` options have different default values. * You can control the output histogram with ``-binw``. * ``-aver`` and ``-averdist`` options are not present. Instead, you can choose between the different things to calculate using ``-oav`` (corresponds to ``-d`` with ``-averdist``), ``-oall`` (corresponds to ``-d`` without ``-averdist``), ``-oh`` (corresponds to ``-o`` with ``-aver``), and ``-oallstat`` (corresponds to ``-l`` without ``-aver``). You can produce any combination of output files. Compared to ``g_bond``, ``gmx distance -oall`` is currently missing labels for the output columns. g_dist ...... **replaced** This tool has been removed in 5.0. A replacement is :ref:`gmx distance` (for most options) or :ref:`gmx select` (for ``-dist`` or ``-lt``). If you had index groups A and B in :file:`index.ndx` for ``g_dist``, you can use the following command to compute the same distance with ``gmx distance``:: gmx distance -n index.ndx -select 'com of group "A" plus com of group "B"' -oxyz -oall The ``-intra`` switch is replaced with ``-nopbc``. If you used ``-dist D``, you can do the same calculation with ``gmx select``:: gmx select -n index.ndx -select 'group "B" and within D of com of group "A"' -on/-oi/-os/-olt You can select the output option that best suits your post-processing needs (``-olt`` is a replacement for ``g_dist -dist -lt``) gmx distance ............ **new** :ref:`gmx distance` has been introduced as a selection-enabled replacement for various tools that computed distances between fixed pairs of atoms (or centers-of-mass of groups). It has a combination of the features of ``g_bond`` and ``g_dist``, allowing computation of one or multiple distances, either between atom-atom pairs or centers-of-mass of groups, and providing a combination of output options that were available in one of the tools. gmx gangle .......... **new** :ref:`gmx gangle` has been introduced as a selection-enabled replacement for ``g_sgangle``. In addition to supporting atom-atom vectors, centers-of-mass can be used as endpoints of the vectors, and there are a few additional angle types that can be calculated. The command also has basic support for calculating normal angles between three atoms and/or centers-of-mass, making it a partial replacement for :ref:`gmx angle` as well. gmx protonate **replaced** This was a very old tool originally written for united atom force fields, where it was necessary to generate all hydrogens after running a trajectory in order to calculate e.g. distance restraint violations. The functionality to simply protonate a structure is available in :ref:`gmx pdb2gmx`. If there is significant interest, we might reintroduce it after moving to new topology formats in the future. gmx freevolume .............. **new** This tool has been introduced in 5.0. It uses a Monte Carlo sampling method to calculate the fraction of free volume within the box (using a probe of a given size). g_sas ..... **rewritten** This tool has been rewritten in 5.0, and renamed to :ref:`gmx sasa` (the underlying surface area calculation algorithm is still the same). The main difference in the new tool is support for selections. Instead of prompting for an index group, a (potentially dynamic) selection for the calculation can be given with ``-surface``. Any number of output groups can be given with ``-output``, allowing multiple parts of the surface area to be computed in a single run. The total area of the ``-surface`` group is now always calculated. The tool no longer automatically divides the surface into hydrophobic and hydrophilic areas, and there is no ``-f_index`` option. The same effects can be obtained by defining suitable selections for ``-output``. If you want output that contains the same numbers as with the old tool for a calculation group ``A`` and output group ``B``, you can use :: gmx sasa -surface 'group "A"' -output '"Hydrophobic" group "A" and charge {-0.2 to 0.2}; "Hydrophilic" group "B" and not charge {-0.2 to 0.2}; "Total" group "B"' Solvation free energy estimates are now calculated only if separately requested with ``-odg``, and are written into a separate file. Output option ``-i`` for a position restraint file is not currently implemented in the new tool, but would not be very difficult to add if requested. g_sgangle ......... **replaced** This tool has been removed in 5.0. A replacement is :ref:`gmx gangle` (for angle calculation) and :ref:`gmx distance` (for ``-od``, ``-od1``, ``-od2``). If you had index groups A and B in index.ndx for ``g_sgangle``, you can use the following command to compute the same angle with ``gmx gangle``:: gmx gangle -n index.ndx -g1 vector/plane -group1 'group "A"' -g2 vector/plane -group2 'group "B"' -oav You need to select either ``vector`` or ``plane`` for the ``-g1`` and ``-g2`` options depending on which one your index groups specify. If you only had a single index group A in index.ndx and you used ``g_sgangle`` ``-z`` or ``-one``, you can use:: gmx gangle -n index.ndx -g1 vector/plane -group1 'group "A"' -g2 z/t0 -oav For the distances, you can use :ref:`gmx distance` to compute one or more distances as you want. Both distances between centers of groups or individual atoms are supported using the new selection syntax. genbox ...... This tool has been split to :ref:`gmx solvate` and :ref:`gmx insert-molecules`. tpbconv ....... This tool has been renamed :ref:`gmx convert-tpr`.