J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....for the spatial decomposition. 1 Overview Molecular dynamics (MD) is a classical mechanics approach typically used to determine the motion of large molecular systems. At the core of the simulation, a force is calculated for each atom from the analytic derivative of a potential energy function [12]. This force displaces the atom from its position in the previous time step. The MD program iterates over a typically large number of time steps in the course of calculating a molecular dynamics trajectory, where the nonbonded force calculation constitutes the bulk of the computational work. Since ....

J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.

.... applied to a molecular dynamics program Before turning to our experience with parallelizing Gromos [6] using the Fortran D compiler, we first give a brief introduction into the underlying application for the examples presented here; for more details, we refer the reader to the literature [2, 10]. Molecular dynamics (MD) is a classical mechanics approach typically used to determine the motion of large molecular systems. At the core of the simulation, a force is calculated for each atom from the analytic derivative of a potential energy function. This force displaces the atom from its ....

J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.

....are consumed in this floating point intensive calculation, and how performance can be degraded by complexities arising in simulating complex molecular systems. 1 The Molecular dynamics calculation Molecular dynamics simulates the motion of a collection of atoms using Newton s equations of motion [20]. A molecular dynamics simulation is considered a chaotic process. In other words, small perturbations on the order of roundoff error can send the simulation into different parts of phase space. This makes it difficult to determine program correctness. Atoms are usually modeled as soft spheres ....

J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.

....of one phase of GROMOS. Section 7 gives some performance results, andin Section 8 we discuss some lessons learned from this project. 2 Molecular Dynamics First developed for simulating atomic motion in simple liquids, molecular dynamics is used routinely to simulate biomolecular systems [15]. Using the compute intensive data obtained from a moleculardynamics simulation, various kinetic, thermodynamic, mechanistic and structural properties can be obtained [16] In molecular dynamics, the motion of each atom, represented as a point mass, is determined by the forces exerted on it by ....

J. Andrew McCammon. Computer-aidedmolecular design. Science, 238:486--491, October 1987.

....must develop an effective parallelization strategy, which requires an in depth understanding of the application for all but the most trivial programs. First developed for simulating atomic motion in simple liquids, molecular dynamics (MD) is used routinely to simulate biomolecular systems [21]. Using compute intensive data obtained from a molecular dynamics simulation, various kinetic, thermodynamic, mechanistic, and structural properties can be obtained [22] Molecular dynamics programs tend to be complex, taking many years to write. Problemdependent parameters, such as the size of a ....

J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.

....6 each describe the parallelization of one phase of GROMOS. Section 7 gives some performance results, followed by conclusions in Section 8. 2 Molecular dynamics First developed for simulating atomic motion in simple liquids, molecular dynamics is used routinely to simulate biomolecular systems [17]. Using the compute intensive data obtained from a molecular dynamics simulation, various kinetic, thermodynamic, mechanistic, and structural properties can be obtained [18] In molecular dynamics, the motion of each atom, represented as a point mass, is determined by the forces exerted on it by ....

J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.

....total number of partners, and MaxAtomP the maximum number of partners per atom. Nchg is the number of charge groups, and MaxChgP the maximum number of partners per charge group. firstAt and lastAt give the range of atoms for a charge group. more details, we refer the reader to the literature [5, 9]. Molecular dynamics (MD) is a classical mechanics approach typically used to determine the motion of large molecular systems. At the core of the simulation, a force is calculated for each atom from the analytic derivative of a potential energy function. This force displaces the atom from its ....

J. A. McCammon. Computer-aided molecular design. Science, 238:486--491, October 1987.

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J. A. McCammon. Computer-aided molecular design. Science, 238:486-- 491, October 1987.

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