Bugs fixed#

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 to let grompp do this.

Issue 4607

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.

Issue 4667

Limit pressure deviations due to missing Lennard-Jones interactions#

For systems dominated by Lennard-Jones interactions, i.e. with no or very weak electrostatics, e.g. most coarse-grained systems, the Verlet buffer was often set such that missing Lennard-Jones interactions could lead to the pressure increasing by more than 1 bar over the lifetime of the pair list. Now an mdp parameter has been added to limit the deviation in the average pressure. The default tolerance is 0.5 bar.

Issue 4861

enemat now prints correct headers when using -free or -eref options#

Fixed a long-standing bug when gmx enemat would output incorrect headers to XVG.

Issue 4812

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.

Issue 4827