Improvements to GROMACS tools

Fixed bug in gmx order -calcdist

The reference position for the distance calculation was calculated wrongly.

Improved grompp usability by rejecting more invalid .mdp lines

Lines like

ref-t 298 = 0.1 =

are now all rejected with a descriptive message, which will help prevent some kinds of errors in constructing .mdp inputs. Note that an .mdp parameter name with a missing value is still accepted, and leads to the default behavior for that parameter.

Added convert-trj

A new tool convert-trj has been added to allow users to interchange trajectory formats without having to use legacy gmx trjconv. Supported actions include the generation of slimmed down output trajectories, as well as the replacement of particle information in individual frames with data from a structure file. The new tool allows the usage of command line selections, meaning it is no longer necessary to write index files to select certain atoms. It is part of the drive to split up the trjconv tool into smaller parts.

Added extract-cluster

Added a dedicated tool to extract trajectory frames corresponding to different clusters obtained from gmx cluster. The new extract-cluster tool generates new trajectories that contain only those frames that correspond to the correct cluster. The corresponding option -sub in gmx trjconv has been removed.

Changed behaviour of genion

Functionality of genion was altered to prevent swapping ions for solvent closer than -rmin from any other non-solvent atom. This improvement prevents situations where an ion could be placed at the core of a protein, which would potentially render the folded protein less stable or may require long equilibration times.