Dear all

I want to visualize a trajectory of a protein with lammpstrj extension in NewCartoon mode in the VMD program, however it is not allowed to visualize any object. Please, what is the correct LAMMPS format to display a protein in VMD? Or maybe it is necessary to convert the trajectory file to another (PDB O PSF)?



This is really more a VMD question than a LAMMPS question. VMD is dependent on residue and force field type information to be able to do advanced protein visualizations. This information is not used by LAMMPS (it uses numeric atom types and has no concept of residues) and thus cannot be output. However you do need this information to generate a LAMMPS data file, e.g. as a .psf file, and VMD can use such a file as well and then will only read coordinates from additional files loaded into the VMD molecule. As a coordinate providing file, you may use lammpstrj dump files or dcd style dump files or xtc style dump files. I would recommend against xyz style dump files, since they are missing the box information, which can be important.