scholarly journals Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1745 ◽  
Author(s):  
Dominik Sidler ◽  
Marc Lehner ◽  
Simon Frasch ◽  
Michael Cristófol-Clough ◽  
Sereina Riniker
Keyword(s):  
Molecular Dynamics ◽  
Weak Coupling ◽  
Stochastic Dynamics ◽  
Md Simulations ◽  
Multiple Time ◽  
Time Step ◽  
Nonbonded Interactions ◽  
Multiple Time Step ◽  
Wide Range ◽  
Dynamics Simulations

Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces for weak coupling and Nosé-Hoover (chain) thermostats. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.

scholarly journals Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1745 ◽  
Author(s):  
Dominik Sidler ◽  
Marc Lehner ◽  
Simon Frasch ◽  
Michael Cristófol-Clough ◽  
Sereina Riniker
Keyword(s):  
Molecular Dynamics ◽  
Weak Coupling ◽  
Stochastic Dynamics ◽  
Md Simulations ◽  
Multiple Time ◽  
Time Step ◽  
Nonbonded Interactions ◽  
Multiple Time Step ◽  
Wide Range ◽  
Dynamics Simulations

Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces for weak coupling and Nosé-Hoover (chain) thermostats. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions or a stochastic dynamics thermostat, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: TR schemes are not advisable to use in combination with weak coupling or Nosé-Hoover (chain) thermostats due to the occurrence of significant numerical artifacts at interfaces.

scholarly journals Density artefacts at interfaces caused by multiple time-step effects in molecular dynamics simulations

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1745 ◽  
Author(s):  
Dominik Sidler ◽  
Marc Lehner ◽  
Simon Frasch ◽  
Michael Cristófol-Clough ◽  
Sereina Riniker
Keyword(s):  
Molecular Dynamics ◽  
Performance Optimization ◽  
Md Simulations ◽  
Multiple Time ◽  
Time Step ◽  
Nonbonded Interactions ◽  
Multiple Time Step ◽  
Wide Range ◽  
Dynamics Simulations ◽  
Interesting Alternative

Background: Molecular dynamics (MD) simulations have become an important tool to provide insight into molecular processes involving biomolecules such as proteins, DNA, carbohydrates and membranes. As these processes cover a wide range of time scales, multiple time-step integration methods are often employed to increase the speed of MD simulations. For example, in the twin-range (TR) scheme, the nonbonded forces within the long-range cutoff are split into a short-range contribution updated every time step (inner time step) and a less frequently updated mid-range contribution (outer time step). The presence of different time steps can, however, cause numerical artefacts. Methods: The effects of multiple time-step algorithms at interfaces between polar and apolar media are investigated with MD simulations. Such interfaces occur with biological membranes or proteins in solution. Results: In this work, it is shown that the TR splitting of the nonbonded forces leads to artificial density increases at interfaces. The presence of the observed artefacts was found to be independent of the interface shape and the thermostatting method used. It is further shown that integration with an impulse-wise reversible reference system propagation algorithm (RESPA) only shifts the occurrence of density artefacts towards larger outer time steps. Using a single-range (SR) treatment of the nonbonded interactions, on the other hand, resolves the density issue for pairlist-update periods of up to 40 fs. Conclusion: A SR scheme avoids numerical artefacts and offers an interesting alternative to TR RESPA with respect to performance optimization.

Advances in biomolecular simulations: methodology and recent applications

2003 ◽  
Vol 36 (3) ◽  
pp. 257-306 ◽  
Author(s):  
Jan Norberg ◽  
Lennart Nilsson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Force Fields ◽  
Md Simulations ◽  
Conformational Space ◽  
Multiple Time ◽  
Time Step ◽  
Field Methods ◽  
Reaction Field ◽  
Dynamics Simulations

1. Introduction 2582. Set-up of MD simulations 2602.1 Constant-pressure dynamics 2602.2 Grand-canonical dynamics 2612.3 Boundary conditions 2613. Force fields 2623.1 Proteins 2623.2 Nucleic acids 2653.3 Carbohydrates 2663.4 Phospholipids 2663.5 Polarization 2674. Electrostatics 2674.1 Spherical truncation methods 2684.2 Ewald summation methods 2694.3 Fast multipole (FM) methods 2714.4 Reaction-field methods 2715. Implicit solvation models 2716. Speeding-up the simulation 2736.1 SHAKE and its relatives 2736.2 Multiple time-step algorithms 2746.3 Other algorithms 2757. Conformational space sampling 2757.1 Multiple copy simultaneous search (MCSS) and locally enhanced sampling (LES) 2757.2 Steered or targeted MD 2767.3 Self-guided MD 2767.4 Leaving the standard 3D Cartesian coordinate system: 4D MD and internal coordinate MD 2777.5 Temperature variations 2778. Thermodynamic calculations 2788.1 Lambda (λ) dynamics 2788.2 Extracting thermodynamic information from simulations 2798.3 Non-Boltzmann thermodynamic integration (NBTI) 2798.4 Other methods 2799. QM/MM calculations 28210. MD simulations of protein folding and unfolding 28310.1 High-temperature effects 28410.2 Co-solvent and polarization effects 28810.3 External force effects 28811. On the horizon 29112. Acknowledgements 29213. References 292Molecular dynamics simulations are widely used today to tackle problems in biochemistry and molecular biology. In the 25 years since the first simulation of a protein computers have become faster by many orders of magnitude, algorithms and force fields have been improved, and simulations can now be applied to very large systems, such as protein–nucleic acid complexes and multimeric proteins in aqueous solution. In this review we give a general background about molecular dynamics simulations, and then focus on some recent technical advances, with applications to biologically relevant problems.

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