Richard J. Loncharich and Bernard R. Brooks. The effects of truncating long-range forces on protein dynamics. PROTEINS: Structure, Function and Genetics, 6:32--45, 1989.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....nonbonded force has been applied. 2 Charge groups The cutoff radius is an approximation used to reduce the number of nonbonded interactions, whose number goes as R 3 cut . Since the Coulomb interaction is proportional to 1 r ij for atoms i and j, the long range effects are non negligible [11]. To improve the cutoff approximation, atoms are grouped into so called charge groups with zero net charge. In this way, the monopole interactions between two charge groups sums to zero, with the nonzero leading term a dipole dipole interaction with 1 r 3 character, thereby reducing the range ....

Richard J. Loncharich and Bernard R. Brooks. The effects of truncating long-range forces on protein dynamics. PROTEINS: Structure, Function and Genetics, 6:32--45, 1989.

....12 A 3 =atom, with the protein more densely packed than the solvent. An average simulation involves about 10,000 atoms in a roughly 50 Theta 50 Theta 50 A 3 box; a simulation with 100,000 atoms or more is considered very large by today s standards. Typical cutoff radii range from 8 A to 20 A [19]. Typical time scales for a simulation range from about 1 picosecond to 1000 picoseconds and are performed with time steps of 1 to 5 femtoseconds. Longer simulations provide better statistics for analysis; given contemporary resources and problem sizes, a 1000 picosecond simulation is considered ....

....the nonbonded force has been applied. Charge groups The cutoff radius is an approximation used to reduce the number of nonbonded interactions, whose number goes as R 3 cut . Since the Coulomb interaction is proportional to 1 r ij for atoms i and j, the long range effects are non negligible [19]. To improve the cutoff approximation, atoms are grouped into so called charge groups with zero net charge. In this way, the monopole interactions between two charge groups sums to zero, with the nonzero leading term a dipole dipole interaction with 1 r 3 character, thereby reducing the range ....

Richard J. Loncharich and Bernard R. Brooks. The effects of truncating long-range forces on protein dynamics. PROTEINS: Structure, Function and Genetics, 6:32--45, 1989.

.... Gamma 15 A. For systems which are significantly larger than this cut off distance the computation of the remaining Coulomb interactions then scales with N instead of N 2 . However, such truncation leads to serious artifacts concerning the description of the structure and dynamics of proteins [44,24,45], and more accurate methods which include the long range interactions should be preferred. Multipole methods and multiple time step methods are well established and widely used for this purpose. We briefly sketch both methods and subsequently show how their combination allows highly efficient ....

Richard J. Loncharich and Bernard R. Brooks. The effects of truncating longrange forces on protein dynamics. Proteins, 6:32--45, 1989.

....particles. However, techniques of this type are not widely used yet in existing molecular dynamics codes. A more common method addressing the N body problem s computational complexity is to consider only nonbonded interactions between atoms which are within a certain cutoff radius of each other [20]. 2.1 The molecular dynamics algorithm The kernels of molecular dynamics programs are often very similar [3, 13, 28] they commonly compute a trajectory through phase space [1] by iterating over the following sequence. 1. Calculate bonded and nonbonded forces on each atom as the analytical ....

....of processors in the range that are available now or in the near future. Our current implementation is aimed for making efficient use of up to 1024 processors. 3. EulerGROMOS is designed for use with a cutoff radius. Historically, the cutoff radius has been used in a tolerable approximation [20]. However, if trends continue, then the problem sizes will continue to outpace hardware capabilities. Furthermore, as simulated biological systems increase in size, the cutoff radius will be more the reasonable, if not desirable, approximation. 4. In transforming GROMOS to EulerGROMOS, we strive ....

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Richard J. Loncharich and Bernard R. Brooks. The effects of truncating long-range forces on protein dynamics. PROTEINS: Structure, Function and Genetics, 6:32--45, 1989.

....sized processor subdomains. Morales and Nuevo decrease the processor subdomain size such that it is less than R cut , but they continue to restrict interactions to neighboring subdomains only, thereby effectively reducing R cut ; they evaluate the effect on thermodynamic properties [16] See [14] for a detailed study on cutoff radius effects. Plimpton also allows for subdomains smaller than R cut in an implementation reported for Lennard Jones particles that is similar to our blockwise decomposition with the Shift algorithm [18] 5 Summary This paper gave a description of EulerGromos, a ....

Richard J. Loncharich and Bernard R. Brooks. The effects of truncating long-range forces on protein dynamics. PROTEINS: Structure, Function and Genetics, 6:32--45, 1989.

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Richard J. Loncharich and Bernard R. Brooks. The effects of truncating long-range forces on protein dynamics. Proteins, 6:32--45, 1989.

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