Unification of box shapes in molecular simulations

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1

Hi!

I had a bit of a theoretical question. Since GROMACS uses a triclinic representation of all boxes, I was wondering if GROMACS uses the methodology from Bekker’s “Unification of box shapes in molecular simulations” when, for example, running gmx trjconv ... -pbc mol -center -ur compact

If so, is there any additional —perhaps more modern—, resource to understand this topic?

Maybe is too of a specific question, but I’d appreciate any pointers. Thanks!

2

We use some of the methodology of that paper. But we don’t use any linear algebra.

The main point to understand is that a periodicity of a system is completely defined by it periodic vectors, which are 3 in the case of a 3D system. How you handle PBC for different parts of the computation is a choice, but doesn’t affect the results. What you can choose is how you want to show a representation of the system.

trjconv -ur compact simply moves each atom along vectors c, b and a (in that order) until the distance to the chosen box center is smallest.

3

aaahhh, and it moves it the same magnitude as the box size in the corresponding direction, right?

So, say, for a given vector from a, b and c and a given particle:
1_calculate the distance to the center
2_move the particle 1 unit of the box dimension along the current cordinate and re-calculate the distance to the center
3_move the particle -1 unit of the box dimension along the current cordinate and re-calculate the distance to the center
Pick the minimum distance among the results of 1, 2 and 3.

And I guess that “particle” may be an atom, a residue or a molecule, to prevent the braking of molecules?

Thanks for taking the time!