Dear LAMMPS users
When I observe .xyz dump files of my simulation box, I see molecules are different and some weird bonds are occurred. On the other hand, by assigning write_data command and visualizing data file with VMD, everything is fine (The bonds and angles are correct).
what is going wrong. It is my fault or It is related to my dump command?
Can I trust to dump files?
thank you so much.
regards.
Reza
Dear LAMMPS users
When I observe .xyz dump files of my simulation box, I see molecules are
different and some weird bonds are occurred. On the other hand, by
assigning write_data command and visualizing data file with VMD, everything
is fine (The bonds and angles are correct).
what is going wrong. It is my fault or It is related to my dump command?
your fault. the .xyz file only contains coordinate information and
numerical atom types. VMD tries to guess bonds by default, but without
usable information, it guesses wrong. data files, however, (can) contain
the full bond topology and that is then used by VMD. since VMD assumes that
the bond topology is explicit and doesn't change, all you need to do is to
extract that bond topology into a suitable file, e.g. a psf. file, and
ideally also tailor the psf file so that it contains correct element, mass,
charge and other information, and then VMD can use the psf file to read the
topology information and then will only need coordinate data for the
trajectory. i recommend against .xyz files, since they contain the least
amount of information. native LAMMPS dump or binary files like .dcd or .xtc
dumps are preferred, as they also contain simulation cell information and
can be tailored more effectively.
axel.
Can I trust to dump files?
yes, if you use them correctly.
dump-data.zip