Journal Article10.1002/JCC.540161009
Reduced variable molecular dynamics
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TL;DR: Application of this methodology is anticipated to provide a 10‐ to 100‐improvement in the speed of a large molecular trajectory as compared with the time required to run a conventional atomistic unconstrained simulation.
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Abstract: Computer simulations of molecular systems provide invaluable insights for understanding the structure—function relationships pertinent to the discovery of new molecules with desired properties, such as new pharmaceutical drugs. The use of molecular simulations and the increasing performance of modern computers makes it now possible to study the precise physicochemical nature of protein—ligand interactions, protein engineering, solvation phenomena, and to characterize the thermodynamical properties of complex systems with many thousands of atoms [1,2]. Even with the availability of high-performance computers, many problems of practical interest are so computationally challenging that new solution methods are required for formulating and solving the resulting mathematical models. This paper explores the capabilities of recursive dynamics methods for reducing the computational effort required for studying complex molecular systems. A numerical example is presented that demonstrates the application of the basic recursive algorithms.
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Citations
Quasi-Hamiltonian Equations of Motion for Internal Coordinate Molecular Dynamics of Polymers
Alexey K. Mazur,Alexey K. Mazur +1 more
TL;DR: In this paper, the authors presented a new method for internal coordinate molecular dynamics simulations of macromolecules, which is applicable to branched chain molecules with any number of internal degrees of freedom.
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•Posted Content
Quasi-Hamiltonian Equations of Motion for Internal Coordinate Molecular Dynamics of Polymers
Alexey K. Mazur,Alexey K. Mazur +1 more
TL;DR: A new method for internal coordinate molecular dynamics simulations of macromolecules is presented which are applicable to branched chain molecules with any number of internal degrees of freedom and use the canonical variables, much simpler than existing analogs.
Canonical ensemble simulation of biopolymers using a coarse-grained articulated generalized divide-and-conquer scheme
TL;DR: The divide-and-conquer algorithm is extended, and applied to constant temperature molecular simulations, and properly accommodates the thermostat generalized forces, which control the temperature of the simulation, in the equations of motion.
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Algorithms for Molecular Dynamics Simulations
Fredrik Hedman
- 01 Jan 2006
TL;DR: Methods for performing large-scale parallel Molecular Dynamics simulations are investigated and a perspective on the field of parallel MD simulations is given.
A separating framework for increasing the timestep in molecular dynamics
Eric Barth,Margaret Mandziuk,Tamar Schlick +2 more
- 01 Jan 1997
TL;DR: In molecular dynamics simulations, the Newtonian equations of motion are solved numerically, and a space/time trajectory of the molecular system is obtained as discussed by the authors, typically, explicit integration algorithms are used: new positions and velocities for all atoms are computed in closed form through simple relations involving positions and velocity at previous steps.
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