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.