Dilek,
The tool places requirements on the extensions of your files. Using the 1ac7 example: in that directory resides 1ac7.data and 1ac7.dump. You can think of these files conforming to project.ext. The project has to be the same for both the LAMMPS data and dump file. The next requirements are that the LAMMPS data file has the extension .data and the dump file has the extension .dump. The 1ac7 example meets these requirements. The project in both cases is the same (1ac7) and there is a 1ac7.data and a 1ac7.dump. You could omit 1ac7.dump if you were only interested in visualizing the contents of 1ac7.data. The existence of a dump file allows you to create the input for a movie by
lammps2pdb.pl –nstart=0 –dn=1 1ac7
This will create a movie starting at frame 0 and adding each following frame. You can review the script’s options by executing just the script name. A ‘chmod +x lammps2pdb.plwill make the script executable and negate the need for typingsource lammps2pdb.pl …`.
Pieter