U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, L. G. Pedersen, A smooth particle mesh ewald method, J. Chem. Phys. 103 (19) (1995) 8577--8593.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....parameters more difficult. At present, there exist several implementations based on this idea, but they differ in detail. In [27] three essential methods are compared and summarized: particle particle particle mesh [54] P M) particle mesh Ewald [26] PME) and smooth particle mesh Ewald [33] (SPME) Unfortunately, the mesh based Ewald methods are affected by errors when performing interpolation, FFT, and differentiation [90] However, it would be misleading to infer that these methods sacrifice accuracy in favor of run time performance. For the fast mesh based Ewald methods, there ....

....be parallelized. On the other hand, the design and development are also user and application driven: 1. Components to implement sophisticated integrators and fast force evaluators, such as MOLLY [44, 45, 58, 59, 60, 62] and Dissipative Molly [82] and multi grid summation [13, 107] PME methods [26, 27, 33, 54], and standard Ewald summation [34] 2. Facilities to compare accuracy of force methods, and to make decisions concerning optimal parameters and method for a given accuracy and system. 3. Components to time performance and analyze parallel scalability. 4. Ability to incorporate methods to ....

U. Essmann, L. Perera, and M. L. Berkowitz. A smooth particle mesh Ewald method. J. Chem. Phys., 103(19):8577--8593, 1995.

.... distance between interacting atoms is used (usually two body interactions are the rate limiting step of the calculation) The use of a cuto# allows reducing the computational expenses but introduces some distortions and inaccuracies that may be partly corrected using Particle Mesh Ewald method [20]. Opposite to implicit water simulations, where the small number of atoms poses strong limitations to the parallelization of the calculation (because of the large amount of communication needed between processors) explicit water simulations with the use of cuto#s allow to take advantage of ....

U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, and L.G. Pedersen. A smooth Particle Mesh Ewald Method. J. chem. phys., 103(19):8577--8593, November 1995.

....interactions which are approximated by a discrete convolution on an interpolating grid, using the 3 dimensional fast Fourier transform (FFT) to efficiently perform the convolution. In the PME method implemented in CHARMM the electrostatic energy is split into direct and reciprocal Ewald sum [4]. The latter is the solution of the Poisson s equation in periodic boundary conditions, with Gaussian charge densities as sources. 2.2 The Molecular System The molecular system used in our simulations is myoglobin, a 153 residue single domain protein of structural class a (i.e. only a helical ....

U.Essmann,L.Perera,M.L.Berkowitz,T.Darden,H.Lee, and L. G. Pedersen. A smooth particle mesh Ewald method. J. Chem. Phys, 103:8577--8593, 1995.

....regard to exclusions, and then correct the interactions between excluded pairs by iterating over a list of those pairs directly. The parallelization of the second step is the role of the exclusion compute objects, which are identical in implementation to the bond compute objects discussed below. 11 There is, unfortunately, one additional complication. While subtracting the electrostatic interaction between bonded atoms is reasonable, adding and subtracting the 1 r 12 repulsive term of the Lennard Jones potential between covalently bonded atoms would result in an unacceptable loss of ....

....of the long range electrostatics of the system, further slowing the calculation. DPMTA is implemented with PVM and hence its incorporation would have been much more di#cult without the multi paradigm capabilities of Converse. 5.1. 3 DPME: Particle Mesh Ewald The particle mesh Ewald (PME) 9, 11] algorithm in NAMD2 is currently based on DPME [46] As the name implies, this method is only applicable for periodic boundary conditions. Similar to particle particle particle mesh (P 3 M) 17, 28, 39] PME divides the electrostatic potential into a local interaction which must be calculated ....

Ulrich Essmann, Lalith Perera, Max L. Berkowitz, Tom Darden, Hsing Lee, and Lee G. Pedersen. A smooth particle mesh Ewald method. J. Chem. Phys., 103(19):8577--8593, 1995.

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U. Essmann, L. Perera, M. L. Berkowitz, T. Darden, H. Lee, L. G. Pedersen, A smooth particle mesh ewald method, J. Chem. Phys. 103 (19) (1995) 8577--8593.

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U. Essmann, L. Perers, M. L. Berkowitz, T. Darden, H. Lee, and L. G. Pedersen. A smooth particle mesh Ewald method. J. Chem. Phys., 103(19), 1995.

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Essmann, U., Perera, L., Berkowitz, M.L.: A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577--8593

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U. Essmann, L. Perera, M. L. Berkowitz, A smooth particle mesh Ewald method, J. Chem. Phys. 103 (19) (1995) 8577--8593.

No context found.

U. Essmann, L. Perera, and M. L. Berkowitz. A smooth particle mesh Ewald method. J. Chem. Phys., 103(19):8577--8593, 1995.

No context found.

Essmann, U., Perera, L., Berkowitz, M.L.: A smooth particle mesh Ewald method. J. Chem. Phys. 103 (1995) 8577--8593

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