Fixes #49

Check for NULL pointers is postponed to class Atoms and is done only if
there are local atoms. This fixes the case where GROMACS put zero atoms in
 a processor and assign a NULL pointer to positions
PlumedMain.cpp: commented line 186 -> this need to be fixed
when a domain of domain decomposition is empty.
Added test on gatindex pointer in class Atoms
Merge branch 'fix-49' into v2.0