8 votes

Minimum image convention for non-orthorhombic unit cells

There is a nice explanation here outlining the difficulties for the minimum image convention in triclinic cells. It describes an exact approach (edit: see discussion below), as well an approximate ...
wcw's user avatar
  • 1,893
8 votes
Accepted

Recalculate atom positions to account for periodic boundary conditions

To visualize the trajectory you can use VMD and use its pbctools vmd trajectory.xyz > pbc set {a b c alpha betta gamma} -all > pbc wrap where ...
Fabian's user avatar
  • 1,411
5 votes

Why should the concept of "nearest/minimum/closest image" even come into the discussion of molecular simulation?

I think you might be missing an important detail about the minimum image convention. Essentially, it tells you which images should be considered as the "real" particle for the purposes of ...
jheindel's user avatar
  • 3,534
5 votes

Recalculate atom positions to account for periodic boundary conditions

You can use ATOMSK. The command: atomsk initial.xyz -wrap final.xyz will wrap all the atom coordinates back into your simulation box. ...
Sufyan's user avatar
  • 683
3 votes

Why should the concept of "nearest/minimum/closest image" even come into the discussion of molecular simulation?

In your own example, the distance from $P'''$ to $P$ is the same as from $P'$ to $P$, namely seven units. So why should $P'$ be the minimum image and not $P'''$? So no, as you yourself have just ...
Shern Ren Tee's user avatar

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