A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations

2006 ◽  
Vol 27 (11) ◽  
pp. 1163-1176 ◽  
Author(s):  
Vincent Kräutler ◽  
Philippe H. Hünenberger
Keyword(s):  
Molecular Simulations ◽  
Multiple Time ◽  
Step Size ◽  
Time Step ◽  
Fast Evaluation ◽  
Nonbonded Interactions ◽  
Time Step Size ◽  
Multiple Time Step ◽  
Distance Dependence ◽  
Step Algorithm

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 Accurate Multiple Time Step in Biased Molecular Simulations

2014 ◽  
Vol 11 (1) ◽  
pp. 139-146 ◽  
Author(s):  
Marco Jacopo Ferrarotti ◽  
Sandro Bottaro ◽  
Andrea Pérez-Villa ◽  
Giovanni Bussi
Keyword(s):  
Molecular Simulations ◽  
Multiple Time ◽  
Time Step ◽  
Multiple Time Step

Calculation of the shear viscosity of decane using a reversible multiple time‐step algorithm

1995 ◽  
Vol 102 (8) ◽  
pp. 3376-3380 ◽  
Author(s):  
Christopher J. Mundy ◽  
J. Ilja Siepmann ◽  
Michael L. Klein
Keyword(s):  
Shear Viscosity ◽  
Multiple Time ◽  
Time Step ◽  
Multiple Time Step ◽  
Step Algorithm

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.

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