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Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems
An N⋅log(N) method for evaluating electrostatic energies and forces of large periodic systems is presented. The method is based on interpolation of the reciprocal space Ewald sums and evaluation ofExpand
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CHARMM: The biomolecular simulation program
TLDR
CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. Expand
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The effect of long‐range electrostatic interactions in simulations of macromolecular crystals: A comparison of the Ewald and truncated list methods
Simulations of the HIV‐1 protease unit cell using a 9 A cutoff, 9/18 A ‘‘twin‐range’’ cutoff, and full Ewald sums have been carried out to 300 ps. The results indicate that long‐range electrostaticExpand
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Solvent structure and hammerhead ribozyme catalysis.
Although the hammerhead ribozyme is regarded as a prototype for understanding RNA catalysis, the mechanistic roles of associated metal ions and water molecules in the cleavage reaction remainExpand
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The fast Fourier Poisson method for calculating Ewald sums
The conventional Ewald expression for the electrostatic energy and forces is recast in a form that can be evaluated to high accuracy in order N log(N) steps using fast Fourier transforms. The fastExpand
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Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation
By utilizing Graphics Processing Units, we show that constant pH molecular dynamics simulations (CpHMD) run in Generalized Born (GB) implicit solvent for long time scales can yield poor pKaExpand
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Cation-Anion Interactions within the Nucleic Acid Ion Atmosphere Revealed by Ion Counting.
The ion atmosphere is a critical structural, dynamic, and energetic component of nucleic acids that profoundly affects their interactions with proteins and ligands. Experimental methods that "count"Expand
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Atomic-level accuracy in simulations of large protein crystals.
Proper treatment of long-range Coulombic forces presents a major obstacle to providing realistic molecular dynamics simulations of macromolecules. Traditional approximations made to lessenExpand
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Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms.
A semiempirical AM1/d Hamiltonian is developed to model phosphoryl transfer reactions catalyzed by enzymes and ribozymes for use in linear-scaling calculations and combined quantumExpand
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Molecular dynamics simulation of HIV-1 protease in a crystalline environment and in solution.
Simulations of the unbound form of the human immunodeficiency virus type 1 protease have been carried out to 200 ps in a crystalline environment and in solution. Solution simulations were performedExpand
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