Trajectory NG: portable, compressed, general molecular dynamics trajectories.
We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on the observation that differences in atomic coordinates/velocities, in either time or space, are generally smaller than the absolute values of the coordinates/velocities. Also, it is often possible to store values at a lower precision. We apply several compression schemes to compress the resulting differences further. The most efficient algorithms developed here use a block sorting algorithm in combination with Huffman coding. Depending on the frequency of storage of frames in the trajectory, either space, time, or combinations of space and time differences are usually the most efficient. We compare the efficiency of our algorithms with each other and with other algorithms present in the literature for various systems: liquid argon, water, a virus capsid solvated in 15 mM aqueous NaCl, and solid magnesium oxide. We perform tests to determine how much precision is necessary to obtain accurate structural and dynamic properties, as well as benchmark a parallelized implementation of the algorithms. We obtain compression ratios (compared to single precision floating point) of 1:3.3-1:35 depending on the frequency of storage of frames and the system studied.
Uppsala Multidisciplinary Center for Advanced Computational Methods (UPPMAX) and Department of Materials Chemistry, Uppsala University, Box 538, SE-751 21 Uppsala, Sweden. daniels@mkem.uu.se
Daniel
D
Spångberg
Daniel S D
DS
Larsson
David
D
van der Spoel
D000465:Algorithms; D044962:Data Compression; D056004:Molecular Dynamics Simulation
J Chem Theory Comput. 2008 Mar;4(3):435-47
26620784
J Chem Inf Comput Sci. 2000 May;40(3):559-66
10850759
Phys Rev A Gen Phys. 1985 Mar;31(3):1695-1697
9895674
J Comput Chem. 2005 Dec;26(16):1781-802
16222654
J Mol Biol. 1984 Aug 25;177(4):735-67
6481804
J Chem Theory Comput. 2008 Jan;4(1):116-22
26619985
J Chem Theory Comput. 2006 Mar;2(2):251-8
26626512
J Chem Theory Comput. 2009 Oct 13;5(10):2798-808
26631792