The effects of truncating long‐range forces on protein dynamics

Proteins: Structure, Function and Bioinformatics - Tập 6 Số 1 - Trang 32-45 - 1989
Richard J. Loncharich1, Bernard R. Brooks1
1Molecular Graphics and Simulation Laboratory, Division of Computer esearch and Technology, National Institutes of Health, Bethesda, Maryland 20892

Tóm tắt

AbstractThis paper considers the effects of truncating long‐range forces on protein dynamics. Six methods of truncation that we investigate as a function of cutoff criterion of the long‐range potentials are (1) a shifted potential; (2) a switching function; (3) simple atom–atom truncation based on distance; (4) simple atom–atom truncation based on a list which is updated periodically (every 25 steps); (5) simple group–group truncation based on distance; and (6) simple group–group truncation based on a list which is updated periodically (every 25 steps). Based on 70 calculations of carboxymyoglobin we show that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. Evaluation of the different methods is based on comparison of a simulation's rms fluctuation about the average coordinates of a no cutoff simulation and from the X‐ray structure of the protein. The simulations in which long‐range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 Å, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function are investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5–9 Å range gives reasonable results for a distance‐dependent dielectric, but not using a constant dielectric. Both the atom–atom and group–group truncation methods based on distance shows large rms deviations and fluctuation for short cutoff distance, while for cutoff distance of 11 Å or greater, reasonable results are achieved. Although comparison of these to distance‐based truncation methods show surprisingly larger rms deviations for the group–group truncation, contrary to simulation studies of aqueous ionic solutions. The results of atom–atom or group–group list‐based simulations generally appear to be less stable than the distance‐based simulations, and require more frequent velocity scaling or stronger coupling to a heat bath.

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Tài liệu tham khảo

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Proteins: Structure, Function and Bioinformatics

Tập 6 Số 1

32-45

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