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Author Walker, Ross C. ♦ Crowley, Michael F. ♦ Case, David A.
Source CiteSeerX
Content type Text
File Format PDF
Subject Domain (in DDC) Computer science, information & general works ♦ Data processing & computer science
Subject Keyword Accurate Qm Mm Potential Method ♦ Qm Mm ♦ Many Nanosecond ♦ Accurate Gradient ♦ Cpu Time ♦ Qm Mm Implementation ♦ Classical Md Simulation ♦ Periodic Explicit Solvent Simulation ♦ Qm System ♦ User Interface ♦ Pddg Mndo Semi-empirical Hamiltonians ♦ Corresponding Classical Simulation ♦ Qm Mm Boundary Show ♦ Pddg Pm3 ♦ Implicit Solvent ♦ Particle Mesh Ewald ♦ Link Atom Approach ♦ Simulation Program ♦ Periodic Boundary
Abstract simulation programs includes a new semi-empirical hybrid QM/MM functional-ity. This includes support for implicit solvent (generalized Born) and for periodic explicit solvent simulations using a newly developed QM/MM implementation of the particle mesh Ewald (PME) method. The code provides suffi-ciently accurate gradients to run constant energy QM/MM MD simulations for many nanoseconds. The link atom approach used for treating the QM/MM boundary shows improved performance, and the user interface has been rewritten to bring the format into line with classical MD simulations. Support is provided for the PM3, PDDG/PM3, PM3CARB1, AM1, MNDO, and PDDG/MNDO semi-empirical Hamiltonians as well as the self-consistent charge density functional tight binding (SCC-DFTB) method. Performance has been improved to the point where using QM/MM, for a QM system of 71 atoms within an explicitly solvated protein using periodic boundaries and PME requires less than twice the cpu time of the corresponding classical simulation.
Educational Role Student ♦ Teacher
Age Range above 22 year
Educational Use Research
Education Level UG and PG ♦ Career/Technical Study