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Molecular Dynamics

  Molecular dynamics consists of solving Newton's equations of motion 

 

where the index i runs through all free (i.e., not fixed) atoms and the gradient is derived from the X-PLOR energy function (Chapter 4). Presently, X-PLOR provides the option to solve Eq. 10.1 in Cartesian coordinate space (Section 10.1) or rigid-body coordinate space (Section 10.2). Molecular dynamics simulations can be stored as trajectory files. Input format, output format, manipulations, and analysis of trajectory files are described in Section 10.





Sat Mar 11 09:37:37 PST 1995