Greetings LAMMPS community,
I have dumped trajectory by dump style “atom”.While visualizing trajectories in VMD,I realized that PBC seems to applied on per atom
because of that many water molecules have bonds across the box.
I am right while interpreting this.If yes,is there any way to write trajectory such that all molecules have correctly placed atoms.
Thanks a lot for your time.
Greetings LAMMPS community,
I have dumped trajectory by dump style "atom".While visualizing trajectories in VMD,I realized that PBC seems to applied on per atom
because of that many water molecules have bonds across the box.
I am right while interpreting this.If yes,is there any way to write trajectory such that all molecules have correctly placed atoms.
your atoms _are_ correctly placed, you can easily recover your desired
selection of periodic images using the pbctools plugin from within VMD.
however, there also are ways to store trajectories in a way that do not
enforce wrapping coordinates back to the principal unit cell.
have a look at the dump_modify command:
for atom style dumps you simply need to turn on the image flag.
if you are using VMD for analysis, it is also highly recommended
to use either the .dcd or .xtc format dumps. they are binary and
load _much_ faster. in that case you would have to turn on unwraping
using dump_modify.
in short. it is all there, you just need to have a closer look
at the documentation.
cheers,
axel.