On 25/02/2012 9:07 PM, ahmet yıldırım wrote:
Dear users,

I am using Gromacs 4.5.4. I rerun the simulation using the following command:
mdrun -s protein-RUN.tpr -cpi protein-RUN.cpt -append
Unfortunately remaining output didnt append to existing files (protein-RUN.xtc, protein-RUN.edr, protein-RUN.log). On the contrary remaining output appended to new files (traj.xtc, ener.edr, md.log).

You told mdrun on the command line to use the default filenames, so it did. Either specify the files you want appended, or use -deffnm suitably. Note that -deffnm cannot supply a name for -cpi.

Mark
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