grompp discourages use of constraints=all-bonds#

Common force fields, including AMBER, CHARMM and OPLS/aa, are parametrized with bonds involving hydrogen constrained. Constraining all bonds should be avoided, for correctness. grompp now issues a note when constraints=all-bonds is used with these force fields when time steps are smaller than 2.6 fs and hydrogens are not replaced by virtual sites. Using constraints=h-bonds will also improve performance.

Documentation changed to reStructuredText#

The complete documentation has been moved to the reStructuredText markup format to allow building it together for display as html or as pdf.