Hello,
I am simulating water flow in a periodic box. To visualize, I output an XTC file. Unfortunately, VMD is unable to show the bonds of molecules at the box boundaries properly because I suspect that when dumping, LAMMPS wraps the coordinates of a molecule even before the whole molecule exits the box. When this happens, VMD shows lines crossing from one end to the other of the box. The bonds of water molecules not near the boundaries are shown properly. I tried outputting the unwrap coordinates and VMD is able to render the bonds properly. However, this is not what I want. I would like to know whether it is possible to make LAMMPS wrap coordinates only when the whole molecule is out of the box. Thank you.
Marcus
Hello,
I am simulating water flow in a periodic box. To visualize, I output an XTC
file. Unfortunately, VMD is unable to show the bonds of molecules at the box
boundaries properly because I suspect that when dumping, LAMMPS wraps the
coordinates of a molecule even before the whole molecule exits the box. When
this happens, VMD shows lines crossing from one end to the other of the box.
The bonds of water molecules not near the boundaries are shown properly. I
tried outputting the unwrap coordinates and VMD is able to render the bonds
properly. However, this is not what I want. I would like to know whether it
is possible to make LAMMPS wrap coordinates only when the whole molecule is
out of the box. Thank you.
no. doing this kind of transformation would require
additional programming. you are most welcome to
contribute such code.
what you can to right now is to use the pbc tools plugin in VMD.
something like:
pbc wrap -component fragment -all
should do the trick.
axel.