New and improved features#
mdrun now also reports the conserved energy quantity with AWH bias sharing#
Added option for setting the ensemble temperature#
Several algorithms, such as pressure coupling and AWH, need the temperature of the system. When not all atoms are coupled to the (same) temperature, it is now possible to tell mdrun what the ensemble temperature is using two new mdp options.
gmxapi.mdrun now publishes the simulation working directory path#
gmxapi.mdrun().output.directory provides the (Future) path to the
working directory/directories for the simulation(s).
This can be useful in conjunction with gmxapi.utility.join_path()
to express data flow based on files known to the user to be produced by
the simulation but not represented by other existing attributes of the
OutputDataProxy.
gmxapi.mdrun now captures STDOUT and STDERR#
The GROMACS library prints a lot of output directly to standard out and
standard error. Previously, this meant that simulator output that traditionally
goes to the terminal would have to be caught from outside the Python
interpreter. In mpi4py based ensembles, it could be challenging to catch the
output at all, without manipulating the mpiexec command line.
gmxapi.mdrun now redirects STDERR and STDOUT during simulation, and provides
paths to the resulting text files on new stdout and stderr outputs.
Reference Issue 4541