M. Eichinger, H. Grubmuller, H. Heller, and P. Tavan. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. J. Comp. Chem., 18:1729--1749, 1997. Home/Search Document Details and Download
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Protein-DNA binding simulation on parallel computers - Korobka (2002) (Correct)
....series are computed apriori to the maximum required degree during the construction of decomposition. Subsequently, evaluation function chooses the effective degree of expansion according to the ratio factor for evaluation point and the expansion sphere. In the description of the FAMUSAMM algorithm [19], Eichinger et al. cite 2 error as sufficient for simulation of electrostatic interactions in the biological systems. This exceeds the precision of the commonly used distance cutoff method which ignores all interactions beyond a specified distance, usually 50 A. Table 4.2 shows the results of ....
M. Eichinger, H. Grubmuller, H. Heller, and P. Tavan. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. J. Comp. Chem., 18:1729--1749, 1997.
Framework Design, Parallelization and Force Computation in.. - Matthey (Correct)
....is already very small for very low temperatures; e.g. for a Ca 40 Coulomb crystal at 1 K the wavelength is of order 10 m, a factor 50 100 smaller than the typical separation distance. sizes certain macroscopic properties of matter can be studied. There is a proliferation of programs for MD [4, 14, 30, 31, 32, 53, 77, 81, 86, 91, 98, 108, 110, 119, 124, 125] and several of these are robust production codes; some with scalable parallel implementations. They cover common MD problems and are excellent tools to perform simulations. However, many of the codes are legacy programs that are either poorly organized or extremely complex. One important factor ....
....number of processors. Atom decomposition based on data replication is an easy but memoryexpensive approach. It has poor scaling properties due to global communication [91] Programs using this decomposition include UHGromos [22] Amber [121] CHARMM [15] Moldy [98] and an early version of EGO [31]. Systolic or hypersystolic loop algorithms [78, 114] are a possible remedy to reduce the memory usage and to improve the scaling. Force decomposition involves either force matrix or systolic loop methods. It scales better than atom decomposition by reducing communication costs through the use ....
M. Eichinger, H. Grubmuller, H. Heller, and P. Tavan. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interactions in molecular dynamics simulations. J. Comp. Chem., 18:1729--1749, 1997.
Conformational Dynamics Simulations of Proteins - Eichinger, Heymann, Heller.. Self-citation (Eichinger Heller Tavan) (Correct)
....potential of those objects, again, can be approximated by their lowest multipole moment. Extending this scheme to higher hierarchy levels, such a structure adapted multipole method (SAMM) provides a substantial speed up for MD simulations as compared to the conventional, grid based methods [38,46]. The performance of this first version of SAMM [36] can be further enhanced by additionally utilizing FMM strategies [34,38] Here, in the vicinity of a given object (e.g. a structural unit or a cluster) the electrostatic potential originating from distant charge distributions is approximated by ....
....between charge groups (structural units and clusters) rather than to the forces acting on individual atoms. In the following we give a short description of this tight and efficient combination. We termed the resulting algorithm FAMUSAMM (multiple time step structure adapted multipole method) [46,47]. A detailed analysis of fast SAMM has shown [47] that the most time consuming tasks are task 2 and task 4 described above. In task 2 for each hierarchy level (except for level 0) a local Taylor expansion is calculated for each object. Note that here we refer to expansions which comprise only ....
M. Eichinger, H. Grubmuller, H. Heller, and P. Tavan. FAMUSAMM: An algorithm for rapid evaluation of electrostatic interaction in molecular dynamics simulations. J. Comp. Chem., 18:1729--1749, 1997.
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