VMD

When I replicate atoms in laamps and then read it by VMD, it makes a bond between two atoms of different molecules because they are closer to each other than a particular distance.
My question is : Does It affect the simulation? and except enhancing the distances how can I solve it?

Reza Khalkhali

Undergraduate student

Polymer & Color Engineering Department

Amirkabir University of Technology

[email protected]…3285…

P.O.Box: 19395-5187 Tehran Iran

Cell phone number: (+98-912)4965625

This is more of a VMD question, but re: LAMMPS,
anything you do in VMD will not affect a LAMMPS simulation.
VMD is simply visualizing what LAMMPS has modeled.

Steve

This is more of a VMD question, but re: LAMMPS,
anything you do in VMD will not affect a LAMMPS simulation.
VMD is simply visualizing what LAMMPS has modeled.

and unless you providing bonding information to VMD
from a LAMMPS data file, those bonds are simply
a geometrical guess based on very limited data.

*you* have to know what you feed LAMMPS to simulate.
if you don't know, you better study your input. VMD is
very deliberately completely ignorant of chemistry and
has all its common sense removed. that is why it is a
good visualization tool, it shows you what *you* tell
it to show, and not what it thinks it should show. the
downside of that is, that the quality, detail, and correctness
of the visualization depends on the quality, detail, and
correctness of the input data you feed it.

cheers,
    axel.