title: Essential Dynamics:  A Tool for Efficient Trajectory Compression and Management.
abstract: We present a simple method for compression and management of very large molecular dynamics trajectories. The approach is based on the projection of the Cartesian snapshots collected along the trajectory into an orthogonal space defined by the eigenvectors obtained by diagonalization of the covariance matrix. The transformation is mathematically exact when the number of eigenvectors equals 3N-6 (N being the number of atoms), and in practice very accurate even when the number of eigenvectors is much smaller, permitting a dramatic reduction in the size of trajectory files. In addition, we have examined the ability of the method, when combined with interpolation, to recover dense samplings (snapshots collected at a high frequency) from more sparse (lower frequency) data as a method for further data compression. Finally, we have investigated the possibility of using the approach when extrapolating the behavior of the system to times longer than the original simulation period. Overall our results suggest that the method is an attractive alternative to current approaches for including dynamic information in static structure files such as those deposited in the Protein Data Bank.
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Tim
authors.initials: T
authors.lastname: Meyer
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Carles
authors.initials: C
authors.lastname: Ferrer-Costa
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Alberto
authors.initials: A
authors.lastname: Pérez
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Manuel
authors.initials: M
authors.lastname: Rueda
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Axel
authors.initials: A
authors.lastname: Bidon-Chanal
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: F Javier
authors.initials: FJ
authors.lastname: Luque
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Charles A
authors.initials: CA
authors.lastname: Laughton
authors.affiliation: Institut de Recerca Biomèdica Barcelona, Parc Científic de Barcelona, Josep Samitier 1-5, Barcelona 08028, Spain, Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain, School of Pharmacy and Centre for Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, U.K., Departament de Bioquímica i Biologia Molecular, Diagonal 645, Barcelona 08028, Spain, Computational Biology Program, Barcelona Supercomputing Center, Jordi Girona 31, Edifici Torre Girona, Barcelona 08028, Spain, and Bioinformatics Structural Node, Instituto Nacional de Bioinformática, Josep Samitier 1-5, Barcelona 08028, Spain.
authors.forename: Modesto
authors.initials: M
authors.lastname: Orozco