diff --git a/gromacs/run.py b/gromacs/run.py index e08edd24..2137d79f 100644 --- a/gromacs/run.py +++ b/gromacs/run.py @@ -94,12 +94,10 @@ class MDrunner(utilities.FileUtils): :attr:`mdrun`. This can be a single string or a sequence (tuple) of strings. On instantiation, the first entry in :attr:`mdrun` that can be found on the :envvar:`PATH` is chosen (with - :func:`find_gromacs_command`). The entries can follow the config file - syntax and denote a *driver* command (for Gromacs 5.x) that is separated - from the command name itself by a colon. For example, ``gmx:mdrun`` from + :func:`find_gromacs_command`). For example, ``gmx mdrun`` from Gromacs 5.x but just ``mdrun`` for Gromacs 4.6.x. Similarly, alternative executables (such as double precision) need to be specified here - (e.g. ``("mdrun_d", "gmx_d:mdrun")``). + (e.g. ``("mdrun_d", "gmx_d mdrun")``). .. Note:: Changing :program:`mdrun` arguments permanently changes the default arguments for this instance of :class:`MDrunner`. (This @@ -109,14 +107,16 @@ class MDrunner(utilities.FileUtils): Added detection of bare Gromacs commands (Gromacs 4.6.x) or commands run through :program:`gmx` (Gromacs 5.x). + .. versionchanged:: 0.6.0 + Changed syntax for Gromacs 5.x commands. """ #: Path to the :program:`mdrun` executable (or the name if it can be found on :envvar:`PATH`); - #: this can be a tuple and then the program names are tried in sequence. You can use - #: the syntax from the config file ``gmx:mdrun`` to designate a driver command. + #: this can be a tuple and then the program names are tried in sequence. For Gromacs 5 + #: prefix with the driver command, e.g., ``gmx mdrun``. #: #: .. versionadded:: 0.5.1 - mdrun = ("mdrun", "gmx:mdrun") + mdrun = ("mdrun", "gmx mdrun") #: path to the MPI launcher (e.g. :program:`mpiexec`) mpiexec = None @@ -278,14 +278,14 @@ def check_success(self): class MDrunnerDoublePrecision(MDrunner): """Manage running :program:`mdrun_d`.""" - mdrun = ("mdrun_d", "gmx_d:mdrun") + mdrun = ("mdrun_d", "gmx_d mdrun") class MDrunnerOpenMP(MDrunner): """Manage running :program:`mdrun` as an OpenMP_ multiprocessor job. .. _OpenMP: http://openmp.org/wp/ """ - mdrun = ("mdrun_openmp", "gmx_openmp:mdrun") + mdrun = ("mdrun_openmp", "gmx_openmp mdrun") mpiexec = "mpiexec" class MDrunnerMpich2Smpd(MDrunner):