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Periodic Boundary Conditions: Files0

Periodic boundary conditions (PBC) are used in molecular dynamics simulations to avoid problems with finite size systems. PBC works by having any atom that leaves the simulation box through one face reenter on the opposite face. This can lead to visual issues where molecules appear to diffuse out of the box or holes form, but these are normal effects of PBC and not problems with the simulation. Tools like trjconv can be used to fix these visual issues after the simulation is completed.

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83 views

Periodic Boundary Conditions: Files0

Periodic boundary conditions (PBC) are used in molecular dynamics simulations to avoid problems with finite size systems. PBC works by having any atom that leaves the simulation box through one face reenter on the opposite face. This can lead to visual issues where molecules appear to diffuse out of the box or holes form, but these are normal effects of PBC and not problems with the simulation. Tools like trjconv can be used to fix these visual issues after the simulation is completed.

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bipin_1986
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Periodic Boundary Conditions - Gromacs http://www.gromacs.org/Documentation/Terminolo...

Periodic Boundary Conditions


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Periodic boundary conditions (PBC) are used in molecular dynamics simulations to avoid problems with boundary
effects caused by finite size, and make the system more like an infinite one, at the cost of possible periodicity
effects.

Beginners visualizing a trajectory sometimes think they are observing a problem when

the molecule(s) does not stay in the centre of the box, or


it appears that (parts of) the molecule(s) diffuse out of the box, or
holes are created, or
broken molecules appear, or
crazy bonds all across the simulation cell appear.

This is not a problem or error that is occuring, it is what you should expect.

The existence of PBC means that any atom that leaves a simulation box by, say, the right-hand face, then enters
the simulation box by the left-hand face. In the example of a large protein, if you look at the face of the simulation
box that is opposite to the one from which the protein is protruding, then a hole in the solvent will be visible. The
reason that the molecule(s) move from where they were initially located within the box is (for the vast majority of
simulations) they are free to diffuse around. And so they do. They are not held in a magic location of the box. The
box is not centered around anything while performing the simulation. Molecules are not made whole as a matter of
course.

These visual issues can be fixed after the conclusion of the simulation by judicious use of the optional inputs to
trjconv to process the trajectory files. Similarly, analyses such as RMSD of atomic positions can be flawed when
a reference structure is compared with a structure that needs adjusting for periodicity effects, and the solution with
trjconv follows the same lines. Some complex cases needing more than one operation will require more than one
invocation of trjconv in order to work.

For further information, see the GROMACS Manual, Chapter 3.

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