11 votes

How to include individual PBC box dimensions in xyz file format compatible with VMD

That is a modification of the standard XYZ file format and is called extended XYZ format, and not all programs are compatible with it. From the VMD Molfile Plugin Documentation page, it looks that VMD ...
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  • 19k
11 votes

What is the meaning of periodic boundary condition for molecular systems?

A periodic boundary condition creates a box around your molecule (or surface) and then treats the molecule leaving the box on the right side as entering the box from the left. This is particularly ...
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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 ...
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  • 1,351
8 votes
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Periodic Boundary Conditions in Atomistic Simulation Environment

The PBC attribute in ASE is used for: finding nearest neighbours input for calculators that may use that information (dftd3, dmol, etc.) creation of surfaces finding the Bravais lattice certain ...
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6 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, as well an approximate algorithm (referencing appendix ...
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  • 1,843
6 votes

How to include individual PBC box dimensions in xyz file format compatible with VMD

Camps is correct, VMD cannot directly parse the comment line of an xyz file because the extended ASE format is not recognized. You can, however, use a tcl-script to load the file and parse the comment ...
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  • 1,351
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. ...
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  • 613
3 votes

How to discard molecules at the boundary in the Atomic Simulation Environment (ASE)?

For an atom in the boundary, the distance with all other atoms of the molecule it is part of will be different based on whether we take into account minimum image convention (MIC) or not. Thus we can, ...
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3 votes
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Why do we even need periodic boundary conditions?

In (Metropolis) Monte Carlo one should be generating random changes in coordinates such that \begin{equation} X_{new} = X_{old} + \Delta X \end{equation} and we used a random number to generate $\...
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  • 4,066
2 votes
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What is the relationship between periodic boundary and the simulation box?

Some pseudo-code ...
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