Internal coordinates for molecular dynamics and minimization in structure determination and refinement

We present a software module which allows one to efficiently perform molecu lar dynamics and local minimization calculations in internal coordinates wh en incorporated into a molecular dynamics package. We have implemented a re ference interface to the NIH version of the X-PLOR structure refinement pac kage and we show that the module provides superior torsion-angle dynamics f unctionality relative to the native X-PLOR implementation. The module has b een designed in a portable fashion so that interfacing it with other packag es should be relatively easy. Other features of the module include the abil ity to define rather general internal coordinates, an accurate integration algorithm which can automatically adjust the integration step size, and a m odular design, which facilitates extending and enhancing the module.