11

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 is only compatible with standard XYZ format. Also, take a look at this answer (to another question) about adding PBC info in VMD after loading standard XYZ ...


9

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 useful for surfaces as otherwise the atoms at the edges (but not on top where you'd be exposed to a solvent) would otherwise degrade into open space. This ...


8

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 a, b, and c are the lattice vectors and alpha, beta, and gamma the angles. The angles can be omitted if the box is orthorhombic. For more information see here: https://www.ks.uiuc.edu/Research/vmd/plugins/...


8

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 constraints certain optimization strategies Nothing is per se changed in the object. But much of the functionality of ASE depends on that attribute. If you are ...


6

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 line yourself. I am no tcl expert but here is an example that works for me: set filename [lindex $argv 0] # load the coordinates into vmd mol new $...


5

You can use ATOMSK. The command: atomsk initial.xyz -wrap final.xyz will wrap all the atom coordinates back into your simulation box. initial.xyz is your input file and final.xyz is the output after wrapping all atoms back into the simulation box. You can get the output in many different formats. ATOMSK is quite powerful and simple to use. Please have a look ...


4

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 C here and Tuckerman appendix B) used by many major molecular dynamics codes. This related discussion is also useful. There is also this question from the ...


3

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, first identify the indices of all the molecules in the structure and then exclude the molecules for which any of the distance is different if MIC is ...


Only top voted, non community-wiki answers of a minimum length are eligible