cg / steep minimizations do not write modified configurations to trajectory
In the trr trajectory written during a minimization, using cg or steep,
all frames except the last one are identical to the starting configuration.
The minimization itself does work, as the energy decreases
and a modified final configuration is found and written.
Observed in Gromacs 4.0.3 on x86-64 running Linux, on a single CPU.
do_cg() in minimize.c gets a t_state state_global.
Modified configurations are stored in a local copy, s_min->s.
Frames are written using write_traj(),
which calls fwrite_trn() for the unmodified state_global.
Only after the minimization loop, copy_em_coords_back()
is called for not-parallel runs ( if (!PAR ),
which updates state_global from s_min->s.
The final frame is written after this, using the modified state_global.
The same problem exists in do_steep().
Calling copy_em_coords_back() after each iteration inside
the minimization loop produces trajectories with updated configurations.