Move virtual site calculation

Move virtual site calculation

The previous implementation would lead to slight inaccuracies when
virtual positions were calculated before shifting positions in
pressure coupling algorithms. This change moves the calculation to the
top of the loop, right before DD and force calculation.

This also removes an unnecessary call to the virtual site construction
in rerun. That call was placed after force calculation and trajectory
writing, so had no influence since coordinates for the next step are
read from file. Since virtual sites are constructed when reading
coordinates from file, the results should have been correct anyway, the
call just had no influence.

This also moves the call to the virtual site construction in MiMiC.
Similar to the rerun case, the current call happened after virtual
sites are used. This call has been moved to right after the coordinates
are received. This is likely to have lead to wrong results when using
MiMiC with virtual sites.

Refs #3866