The deform option was unsuited for flow simulations#
The deform option now only deforms the box and does not modify atom positions
anymore. In contrast to previous versions, it instead corrects the velocities
of particles when they are shifted by a periodic box vector. Now, deform is
also useful for shear flows. Applications where the system was stretched until
some interactions broke were probably not affected measurably by
these issues. Note that a velocity profile should be generated when using
deform with the current or later versions. An mdp option has been added
grompp do this.
mdrun now checks for excluded pairs beyond the cut-off with reaction-field and FEP#
With reaction-field electrostatics and free-energy calculations, excluded atom pairs are not allowed to be beyond the Coulomb cut-off distance. Now mdrun checks for this and throws an error when this occurs.
enemat now prints correct headers when using
Fixed a long-standing bug when
gmx enemat would output incorrect headers
gmxapi.commandline_operation implicitly converts input_files to absolute paths#
Relative paths in the input_files mapping are now explicitly relative to the working directory of the caller.