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Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories.

ABSTRACT: Molecular dynamics (MD) simulations are now able to routinely reach timescales of microseconds and beyond. This has led to a corresponding increase in the amount of MD trajectory data that needs to be stored, particularly when those trajectories contain explicit solvent molecules. As such, it is desirable to be able to compress trajectory data while still retaining as much of the original information as possible. In this work, we describe compressing MD trajectory data using the NetCDF4/HDF5 file format, making use of quantization of the original positions to achieve better compression ratios. We also analyze the affect this has on both the resulting positions and the energies calculated from post-processing these trajectories, and recommend an optimal level of quantization. Overall we find the NetCDF4/HDF5 format to be an excellent choice for storing MD trajectory data in terms of speed, compressibility, and versatility.

SUBMITTER: Roe DR

PROVIDER: S-EPMC9703595 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories.

Roe Daniel R DR Brooks Bernard R BR

Protein science : a publication of the Protein Society 20221201 12

Molecular dynamics (MD) simulations are now able to routinely reach timescales of microseconds and beyond. This has led to a corresponding increase in the amount of MD trajectory data that needs to be stored, particularly when those trajectories contain explicit solvent molecules. As such, it is desirable to be able to compress trajectory data while still retaining as much of the original information as possible. In this work, we describe compressing MD trajectory data using the NetCDF4/HDF5 fil ...[more]

PMID: 36382864

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Project description:We present here a greatly updated version of an earlier study on the conformational energies of protein-ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. Bioorg. Med. Chem. 1995, 3, 411-428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a "high-quality" subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G(d) basis set and a single-point energy calculation at B3LYP/6-311++G(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most "conservative" choice of all the possible conformational energies-the energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformer-significant energy values were found. The range of 0 to ~25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of "outliers" of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R(free)-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient (RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy.

Dataset Information

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories.

Publications

Quantifying the effects of lossy compression on energies calculated from molecular dynamics trajectories.

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