An efficient and extensible format, library, and API for binary trajectory data from molecular simulations

Journal of Computational Chemistry

Volumn 35, Issue 3, 2014, Pages 260-269

  Lundborg, Magnus ^a   Apostolov, Rossen ^a,b   Spångberg, Daniel ^b   Gärdenäs, Anders ^c   Van Der Spoel, David ^c   Lindahl, Erik ^a,c  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b UPPSALA UNIVERSITY   (Sweden)

^c STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

API; compression; file format; molecular dynamics simulation

Indexed keywords

API; COMPRESSION ALGORITHMS; FILE FORMATS; HIGH-PERFORMANCE COMPUTING RESOURCES; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; SIMULATION PROJECTS; THEORETICAL CHEMISTRY;

APPLICATION PROGRAMS; COMPACTION; MOLECULAR DYNAMICS;

DIGITAL STORAGE;

2 NAPHTHYLAMINE; ACETAMIDE DERIVATIVE; ALCOHOL; DRUG DERIVATIVE; N ACETYLALADANAMIDE; N-ACETYLALADANAMIDE; POTASSIUM CHANNEL KV1.2; RIBONUCLEASE; ZEBRAFISH PROTEIN;

ALGORITHM; ANIMAL; API; ARTICLE; CHEMISTRY; COMPRESSION; COMPUTER PROGRAM; FILE FORMAT; INFORMATION PROCESSING; MOLECULAR DYNAMICS; STANDARD; ZEBRA FISH;

API; COMPRESSION; FILE FORMAT; MOLECULAR DYNAMICS SIMULATION;

2-NAPHTHYLAMINE; ACETAMIDES; ALGORITHMS; ANIMALS; AUTOMATIC DATA PROCESSING; ETHANOL; KV1.2 POTASSIUM CHANNEL; MOLECULAR DYNAMICS SIMULATION; RIBONUCLEASES; SOFTWARE; ZEBRAFISH; ZEBRAFISH PROTEINS;

EID: 84891344337     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23495     Document Type: Article

References (24)

1. List of Software for Molecular Mechanics Modeling. Available at: http://en.wikipedia.org/w/index.php?title=List-of-software-for-molecular- mechanics-modeling&oldid=564406774. Accessed on November 17, 2013.
2. R. Salomon-Ferrer, D. Case, R. Walker, WIREs Comput. Mol. Sci. 2013, 3, 198.
3. The Amber Molecular Dynamics Package. Available at: http://ambermd.org/. Accessed on November 17, 2013.
4. R. Rew, G. Davis, IEEE Comput. Graph. Appl. 1990, 10, 76.
5. S. A. Brown, M. Folk, G. Goucher, R. Rew, Comput. Phys. 1993, 7, 304.
6. Unidata | NetCDF. Available at: http://www.unidata.ucar.edu/software/ netcdf/. Accessed on November 17, 2013.
7. B. R. Brooks, C. L. Brooks, III, A. D. MacKerell Jr., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comput. Chem. 2009, 30, 1545.
8. File formats. Available at: http://www.ks.uiuc.edu/Research/namd/2.6/ug/ node13.html. Accessed on November 17, 2013.
9. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kalé, K. Schulten, J. Comput. Chem. 2005, 26, 1781.
10. NAMD-Scalable Molecular Dynamics. Available at: http://www.ks.uiuc.edu/ Research/namd/. Accessed on November 17, 2013.
11. A. T. Brünger, P. D. Adams, G. M. Clore, W. L. DeLano, P. Gros, R. W. Grosse-Kunstleve, J. -S. Jiang, J. Kuszewski, M. Nilges, N. S. Pannu, R. J. Read, L. M. Rice, T. Simonson, G. L. Warren, Acta Crystallogr. D Biol. Crystallogr. 1998, 54, 905.
12. K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, D. E. Shaw, In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing, ACM: New York, 2006.
13. D. E. Shaw Research. Available at: http://www.deshawresearch.com/ resources-desmond.html. Accessed on November 17, 2013.
14. Desmond Users Guide, Section 13.1, Desmond Molecular Dynamics System, Version 3.4.0/0.7.2, D. E. Shaw Research: New York, 2013.
15. B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, J. Chem. Theory Comput. 2008, 4, 435.
16. S. Pronk, S. Páll, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. van der Spoel, B. Hess, E. Lindahl, Bioinformatics 2013, 29, 845.
17. D. G. Green, K. E. Meacham, M. Surridge, F. van Hoesel, H. J. C. Berendsen, In Methods and Techniques in Computational Chemistry: METECC-95;, E. Clementi, G. Corongiu, Eds.; STEF: Cagliari, 1995; pp. 435-463.
18. S. Plimpton, J. Comput. Phys. 1995, 117, 1.
19. LAMMPS Molecular Dynamics Simulator. Available at: http://lammps.sandia. gov/. Accessed on November 17, 2013.
20. D. Spångberg, D. S. D. Larsson, D. van der Spoel, J. Mol. Model. 2011, 17, 2669.
21. T. Meyer, C. Ferrer-Costa, A. Pérez, M. Rueda, A. Bidon-Chanal, F. J. Luque, C. A. Laughton, M. Orozco, J. Chem. Theory Comput. 2006, 2, 251.
22. N. A. Murugan, R. Apostolov, Z. Rinkevicius, J. Kongsted, E. Lindahl, H. Ågren, J. Am. Chem. Soc. 2013, 135, 13590.
23. P. Bjelkmar, P. S. Niemelä, I. Vattulainen, E. Lindahl, PLoS Comput. Biol. 2009, 5, e1000289.
24. Command-Line Trajectory Conversion: mdconvert. Available at: http://mdtraj.s3.amazonaws.com/mdconvert.html. Accessed on November 17, 2013