Long range Debye-Hückel correction for computation of grid-based electrostatic forces between biomacromolecules
Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and ener...
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| Main Authors: | , , |
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| Format: | Article (Journal) |
| Language: | English |
| Published: |
17 June 2014
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| In: |
BMC Biophysics
Year: 2014, Volume: 7, Issue: 1 |
| ISSN: | 2046-1682 |
| DOI: | 10.1186/2046-1682-7-4 |
| Online Access: | Verlag, lizenzpflichtig, Volltext: https://doi.org/10.1186/2046-1682-7-4
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| Author Notes: | Paolo Mereghetti, Michael Martinez and Rebecca C. Wade |
MARC
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| 520 | |a Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to contain the computational costs, especially for the computation of interaction forces and energies. A common approach is to compute interaction forces between macromolecules by precomputing their interaction potentials on three-dimensional discretized grids. For long-range interactions, such as electrostatics, grid-based methods are subject to finite size errors. We describe here the implementation of a Debye-Hückel correction to the grid-based electrostatic potential used in the SDA BD simulation software that was applied to simulate solutions of bovine serum albumin and of hen egg white lysozyme. | ||
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