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Hi Mostafa
You can also try the (stand-alone) program xyz2dcd (https://github.com/cp2k/cp2k/blob/master/src/motion/xyz2dcd.F) from the current cp2k trunk which dumps the frames from a CP2K xyz trajectory file in dcd format optionally with wrapped coordinates (flags –pbc and –pbc0) using either fixed cell parameters (flags –abc and –cell) or the actual cell information for each frame from the corresponding CP2K cell file of the same NpT run, e.g. by running
xyz2dcd –pbc –cell_file project-1.cell project-pos-1.xyz >project-pos-1_wrapped.dcd
The generated binary file project-pos-1.dcd in DCD format with wrapped coordinates and the corresponding cell information for each frame can be loaded into VMD or converted again back to xyz (XMOL) format using
dumpdcd -xyz project-pos-1.xyz –of XMOL –o project-pos-1_wrapped.xyz project-pos-1_wrapped.dcd
xyz2dcd and dumpdcd are compiled automatically with the current CP2K trunk version and can be found then in folder cp2k/exe/<arch>/, but they can also be compiled independently, e.g. using
gfortran –ffree-form –o xyz2dcd xyz2dcd.F
The flag –h provides further usage info.
HTH
Matthias
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