Restart the simulation from a checkpoint file . . .

http://www.gromacs.org/Documentation/How-tos/Doing_Restarts

Thank you dear Martin. I have already read that. It said how to achieve a checkpoint while MDS is crashed. I want to perform MDS with long mdrun yet not at the first step.

Energy minimization is not that important. However, if you change cut-offs it is better to perform a short equilibration simulation. But if you change thermostat, you do not need to do so. It all depend what you going to change in mdp file.