Bugs fixed

Fixed slight inaccuracies when using virtual sites with pressure coupling

Virtual sites were reconstructed after the system was propagated, but before scaling due to pressure coupling. For virtual site types which are not a linear combination of other atoms, this is not completely correct. Since the scaling due to pressure coupling is very small in healthy simulations, the resulting inaccuracies are expected to have been extremely minor, and in most cases undetectable.

Issue 3866

Correct dVremain/dl when nstdhdl > nstcalcenergy

When nstcalcenergy was not a multiple of nstdhdl, incorrect dVremain/dl terms were written in the energy file. Note that all dH/dl output in both dhdl.xvg and the energy file, which is used by e.g. gmx bar, was correct.

Removed velocity output for acceleration groups

The reported velocity in the energy file for acceleration groups was always zero. Now their velocity is no longer reported in the energy file.

Issue 1354

Use correct c0 parameter in Me2PO4 in OPLSAA

OPLSAA torsions must sum to 0, but the parameters for Me2PO4 did not do so. Changed the c0 parameter to the correct value.

Issue 4075

Allow function type Fourier Dihedral with free energy perturbations

The Fourier Dihedral (dihedral interaction type 3) could not be used in free energy perturbation simulations. Under the hood the dihedral parameters were anyhow converted to Ryckaert-Bellemans parameters, so now the checks for perturbations are the same for the two functions.

Issue 2606

Do not scale coordinates of frozen atoms during Parrinello-Rahman pressure coupling

When Parrinello-Rahman pressure coupling was used, the box scaling was applied to all the atoms, causing frozen atoms to shift. The effect is more drastic towards the sides of the box and when the pressure is changed significantly during the simulations. Now, the frozen atoms will be ignored by the coupling and atoms with frozen dimensions shall keep such values.

Issue 3075

Avoid non-uniform rotation with Test Particle Insertion in anisotropic systems

With anisotropic systems the random angles would not get a uniform distribution.

Issue 3558

Allow free energy calculations with a linear angle potential

Free energy calculations with a linear angle potential were not explicitly allowed by grompp.

Issue 3456

Fixed progress display in trjconv and trjcat

The progress information (frame number and time) shown during trajectory operations in trjconv and trjcat is now correctly displayed.

Issue 4320

Fixed GROMOS dihedral generation for disulfide bridges

The pdb2gmx functionality now generates correct dihedrals for disulfide bridges with the GROMOS force field series.

Issue 4188

Fixed energy term naming for periodic improper dihedrals

Those used the same name internally as the non-periodic version for printing to energy files and reading from them. This could cause tools being confused when trying to compare terms from files where the terms where written in a different order.

gmx density now always uses relative coordinates

There is no realistic use case for using absolute coordinates in binning when the box dimension is changing, so gmx density now always uses relative coordinates internally. This also avoids issues with output scaling to the last instead of average box size when users forget this option, ensures the output is always correct, and gets rid of occassional segfaults.

Issue 3830