Questions tagged [minimum-image-convention]
"The minimum-image convention is a common form of PBC particle bookkeeping in which each individual particle in the simulation interacts with the closest image of the remaining particles in the system."
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Are there any codes generating clusters of molecules?
I wanted to generate clusters containing 5 or 6 molecules, are there any python packages which take in an input xyz file and provide me with such cluster systems?. Just wanted to check to avoid re-...
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How to find the scaling factors for minimum image convention?
Suppose that we have an arbitrary (not necessarily cubic) unit cell with cell parameters $\mathbf{a}$, $\mathbf{b}$, $\mathbf{c}$ (lattice vectors) and $\alpha$, $\beta$, $\gamma$ (lattice angles).
We ...
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Why should the concept of "nearest/minimum/closest image" even come into the discussion of molecular simulation?
Suppose, I have a 2D simulation box whose corners are $A(-2,-1)$, $B(-2, 4)$, $C(5,4)$, $D(5,-1)$; I have a particle $P(6, 3)$ inside the simulation box.
The $X$ dimension of the box: $7$.
Therefore,
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Minimum image convention for non-orthorhombic unit cells
I am trying to take into account periodic boundary conditions for non-orthorhombic unit cells.
I have the atomic coordinates for a monoclinic super cell with the following lattice vectors output by ...
user2026
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Recalculate atom positions to account for periodic boundary conditions
I have the output of a simulation done using Periodic boundary conditions (PBC), however, the atom positions have been resolved, i.e. there are atoms outside the PBC-box now. Is there a software/...
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