Taming the Ewald sum in molecular dynamics simulations of solvated proteins via a multiple time step algorithm

1996 ◽  
Vol 104 (8) ◽  
pp. 3003-3012 ◽  
Author(s):  
Piero Procacci ◽  
Massimo Marchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Multiple Time ◽  
Time Step ◽  
Ewald Sum ◽  
Multiple Time Step ◽  
Step Algorithm ◽  
Dynamics Simulations

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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