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Theory and implementation

It is often of interest to separate global motion from internal motion, both for quantitative analysis and for visualization by animated display. Obviously, this can be done under the hypothesis that global and internal motions are decoupled within the length and timescales of the analysis. nMOLDYN can create GMFT by filtering out global motions (made of the three translational and rotational degrees of freedom), either on the whole system or on an user-defined subset, by fitting it to a reference structure (usually the first frame of the MD). Global motion filtering uses a straightforward algorithm:

- for the first frame, find the linear transformation such that the coordinate origin becomes the center of mass of the system and its principal axes of inertia are parallel to the three coordinates axes (also called principal axes transformation),
- this provides a reference configuration ,
- for any other frames f, finds and applies the linear transformation that minimizes the RMS distance between frame f and .

The result is stored in a new trajectory file that contains only internal motions. This analysis can be useful in case where diffusive motions are not of interest or simply not accessible to the experiment (time resolution, powder analysis ...).

Next: Parameters Up: Global Motion Filtered Trajectory Previous: Global Motion Filtered Trajectory Contents