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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 ...
Camps's user avatar
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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 ...
Raz Jugovic's user avatar
8 votes
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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
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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 ...
nickpapior's user avatar
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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
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8 votes
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Clustering Algorithms with Periodic Boundary Conditions

First, there is a recent paper in which they proposed a k-means clustering algorithm adapted for periodic boundary conditions. Their Python implementation is available here. However, the clustering ...
Shaun Han's user avatar
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7 votes
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Unwrapping particle coordinates in MD simulations to remove effects of periodic boundary condition

When you are doing an MD simulation, you should ideally be using a large simulation box so that you can study the properties of the system. However, this is easier said than done because of the ...
Hemanth Haridas's user avatar
7 votes
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How to model an isolated molecule with Quantum ESPRESSO?

Quantum Espresso, like all plane-wave DFT software (e.g. ABINIT, CASTEP, VASP), has to have periodic boundary conditions, because the plane-waves themselves are periodic. When you want to study ...
Phil Hasnip's user avatar
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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 ...
Fabian's user avatar
  • 1,421
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
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5 votes
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What is the difference between a "periodic image" and a "nearest image" in MD simulation?

You can generate a periodic image n times in any direction. In comparison, the nearest image is the one that is calculated as +x or -x in the x-direction, +y or -y in the y-direction and +z or -z in ...
Hemanth Haridas's user avatar
4 votes
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What is the relationship between periodic boundary and the simulation box?

Some pseudo-code ...
B. Kelly's user avatar
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4 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 $\...
B. Kelly's user avatar
  • 4,366
4 votes

What is the difference between a "periodic image" and a "nearest image" in MD simulation?

In the general case, we have lattice vectors ${\bf L}_{i}$, which may not be orthogonal. With periodic boundary condition, a particle at ${\bf r}$ has periodic images at ${\bf r}+n_1{\bf L}_1+n_2{\bf ...
Susi Lehtola's user avatar
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3 votes
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Is there any effect on the physical properties when the size of the system increases in DFT?

This is a partial answer to your question. Here I discuss the effect of the size of supercell on DOS, PDOS, and band structure. Others can add the effect on optical or other electronic properties. As ...
Abdul Muhaymin's user avatar
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, ...
Rashid Rafeek's user avatar
3 votes
Accepted

Verifying periodicity of crystalline orbital modulus in PySCF

Setting the unit='Bohr' flag in gto.M (as originally suggested in the comments) resolved the issue in the latest version of the ...
phonon's user avatar
  • 61
2 votes

Symmetric issue about the Gaussian basis Hamiltonian

The simplest way of putting this is to note that the Hamiltonian is an operator corresponding to an observable (the energy) and hence by the postulates of quantum mechanics must be Hermitian. In the ...
Ian Bush's user avatar
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