Fix type bug in trilinic DD code#
Fix bug with unusual off-diagonal elements communicating too few atoms.
Ensure domains are large enough for atom motion#
Domain decomposition now makes sure that domains will always be large enough so that atoms will not move across additional domains.
Velocity Verlet integrators output energy averages from correct steps#
Velocity Verlet integrators would accumulate energies for writing averages to the energy file when step-1 was a multiple of nstcalcenergy. This has now been corrected to step being a multiple of nstcalcenergy. Note that although this (slightly) changes the reported averages, the averages were not incorrect.
Fix chainsep behaviour of pdb2gmx#
grompp correctly checks nstexpanded against nstcalcenergy#
With expanded ensemble, but without free-energy perturbation, grompp would not check if nstexpanded was a multiple of nstcalcenergy. If the latter was not the case, results might have been incorrect.
Issue with do_dssp and unknown residues#
The do_dssp tool would fail with unknown residues, as well as have issues on Windows.