New features

• Exact restarts are now also possible with temperature and pressure coupling. To achieve this coupling data is written to the energy file, which can be passed to tpbconv and grompp. A parameter init_step has been added to the mdp file so also the step numbers can be continued.
   
• Conjugate gradient minimization uses a new, more efficient algorithm: Polak-Ribiere.
   
• A new random number generator has been implemented which uses a state of 624 numbers. It should never cycle in practice.
   
• The random Gaussian number generator now uses a table lookup which is at least an order of magnitude faster than the old one. This speeds up BD and SD simulations of simple systems significantly.
   
• Complete rewrite of the pull code. The forces are now corrected for mass-weighting when dynamic pull-groups are used. There are some new features with constraint pulling.
   
• With shift and switch potentials rlist is now allowed to be larger than rcoulomb and rvdw.
   
• Dispersion correction can now also be applied to switched potentials (Note that in 3.2.0 and 3.2.1 the virial correction is incorrect, but the pressure correction is correct).
   

Bug fixes

• A bug has been fixed with PME and triclinic boxes that have angles that are far from 90 degrees, such as a rhombic dodecahedron and a trucated octahedron. When a molecule larger than half the box-size would be at the edge of the box the periodicity was not taken into account correctly.
   
• A bug has been fixed which could cause some LJ interactions at distances close to rvdw to be neglected when rvdw > rcoulomb (in practice this would only occur with GROMOS forcefields combined with PME).