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Molecular dynamics trajectory compression with a coarse-grained model.

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 is 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.

SUBMITTER: Cheng YM

PROVIDER: S-EPMC3505254 | biostudies-literature | 2012 Mar-Apr

REPOSITORIES: biostudies-literature

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Molecular dynamics trajectory compression with a coarse-grained model.

Cheng Yi-Ming YM Gopal Srinivasa Murthy SM Law Sean M SM Feig Michael M

IEEE/ACM transactions on computational biology and bioinformatics 20111017 2

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 is 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]

PMID: 22025759

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