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Dynamic bond constraints in protein Langevin dynamics

Authors: J, Franklin; S, Doniach;

Dynamic bond constraints in protein Langevin dynamics

Abstract

Bond constraint algorithms for molecular dynamics typically take, as the target constraint lengths, the values of the equilibrium bond lengths defined in the potential. In Langevin form, the equations of motion are temperature dependent, which gives the average value for the individual bond lengths a temperature dependence. In addition to this, locally constant force fields can shift the local equilibrium bond lengths. To restore the average bond lengths in constrained integration to their unconstrained values, we suggest changing the constraint length used by popular constraint methods such as RATTLE [H. C. Andersen, J. Comput. Phys. 52, 23 (1983)] at each step. This allows us to more accurately capture the equilibrium bond length changes (with respect to the potential) due to the local equilibration and temperature effects. In addition, the approximations to the unconstrained nonbonded energies are closer using the dynamic constraint method than a traditional fixed constraint algorithm. The mechanism for finding the new constrained lengths involves one extra calculation of the bonded components of the force, and therefore adds O(N) time to the constraint algorithm. Since most molecular dynamics calculations are dominated by the O(N2) nonbonded forces, this new method does not take significantly more time than a fixed constraint algorithm.

Related Organizations
Keywords

Proteins, Hydrogen Bonding, Models, Theoretical, Algorithms

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
2
Average
Average
Average
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