Abstract
This paper presents an analysis of molecular dynamics towards an understanding of the contribution of slow and fast modes and proposes an integration method, the “Subspace Molecular Dynamics”. The analysis of exact molecular dynamics for biological polymers reveals that only a very small proportion of the slow motion modes, of the order to a few percent to ten percent, participate in the fundamental dynamics. Furthermore, the calculations presented in this paper indicate that the system remains in subspaces for relatively long times of the order of picoseconds. Both of these observations suggest that one could implement these ideas in working directly with the subspace. The major difficulty is that although the system evolves in a low dimensional subspace, the basis vectors defining this subspace rotate in time.
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