Molecular Dynamics Trajectory Compression with a Coarse-Grained Model

Authors:
Yi-Ming Cheng;Srinivasa Murthy Gopal;Sean M. Law;Michael Feig
Affiliations:
Michigan State University, East Lansing;Michigan State University, East Lansing;Michigan State University, East Lansing;Michigan State University, East Lansing
Venue:
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Year:
2012

Citing 4
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Data compression

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Abstract

Molecular dynamics trajectories are very data intensive thereby limiting sharing and archival of such data. One possible solution is compression of trajectory data. Here, trajectory compression based on conversion to the coarse-grained model PRIMO is proposed. The compressed data are about one third of the original data and fast decompression is possible with an analytical reconstruction procedure from PRIMO to all-atom representations. This protocol largely preserves structural features and to a more limited extent also energetic features of the original trajectory.