[gmx-users] why gromacs cannot repeat out the results?

[范聪]

Hello, everyone!
 I've run two molecular dynamics using gromacs with exactly the same inputs, in the very same computer, and there's no radom process such as velocity distribution.( I've used "mdrun -t nvt.cpt" to stop a new velocity distribution)
 Now I'm puzzled that gromacs have output two results of great differences, both in the trajectory and in the energy calculation results. Now I don't know which one to trust.
I've learned that Molecular Dynamics software solve Newton equitations to decide the movement of atoms, and calculate the potential energy according to the location of each atom.
So how could it happen that the very same inputs generate so different results?
Could there be some way to  avoid all above?