Thanks chris for your answer. I'm using Gromacs 4.6.3 with AMBER03 force field. i had a 20ns run with this command:mdrun -s .tpr -v -deffnm but after some days and passing less than 4 ns of run, power turned out and the run was crashed. i used this command to restart the run:mdrun -s .tpr -v -deffnm newmd -cpi .cpt -appendafter finnishing all 20ns of run i calculated RMSD and H-bonds and i noticed that there are times at the bigining of second part which are common with the end times of first part, but the results of RMSD and H-bonds in these times does not match.I have had the same experience using Gromacs 4.6.7 -- Gromacs Users mailing list
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