P. K. Weiner and P. A. Kollman. Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....of CHAOS that can be used to support efficient execution of irregular problems on distributed memory machines. This work was sponsored in part by ARPA (NAG 1 1485) and NSF (ASC 9213821) 1 Introduction Molecular dynamics (MD) simulation programs, such as CHARMM [1] GROMOS [2] and AMBER [3], are useful to study the structural, equilibrium, and dynamic properties of molecules. These programs are very complicated and computationally intensive. Implementing them on massively parallel processing systems not only reduces execution times but also allows users to solve larger problems. In ....

P. K. Weiner and P. A. Kollman. Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981.

....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 ....

....dominate, since the integration is relatively cheap to carry out. Nevertheless, the terms of the sum of interactions U( x 1 ; x 2 ; x N ) are independent. Altogether, this makes MD to a certain extent inherently parallel.This has been exploited by several parallel MD programs [4, 14, 22, 23, 32, 53, 77, 81, 86, 91, 98, 110, 124, 125]. When parallelizing MD, there are two important considerations to make. First, the MD program must perform well for a small number of particles, i.e. less than 1000. There are several interests to carry out simulations with a few thousand particles over a long time scale, e.g. a protein ....

P. K. Weiner and P. A. Kollman. AMBER: Assisted model building with energy refinement. a general program for modeling molecules and their interactions. J. Comp. Chem., 2:287, 1981.

.... operation counts for NAMD on benchmark systems and simulation modes cuto# (Cut) PME every step (PME) and multiple timestepping with PME every four steps (MTS) 6 Benchmark Methodology NAMD is a production simulation engine, and has been benchmarked against the standard community codes AMBER [13] and CHARMM [2] The serial performance of NAMD is comparable to these established packages, while its scalability is much better. NAMD is an optimized and e#cient implementation of the MD algorithm as applied to biomolecular systems. In order to demonstrate the scalability of NAMD for the real ....

P. K. Weiner and P. A. Kollman. AMBER: Assisted model building with energy refinement. A general p rogram for modeling molecules and their interactions. J. Comp. Chem., 2(3):287--303, 1981. 18

....or 4 aa, where it might overly constrain the folding of the protein. Because each processor would vary the dihedral angles (and possibly the principal side chain angles) only of the residues in the coils and turns, the simulation would run quickly enough to be guided by a realistic energy function [14, 15, 16, 17] with solvation and excluded volume. At the end of a run of perhaps 100,000 sweeps, the final energies of the di#erent secondary structures would be compared and their folds stored. Many runs would be required to test all the plausible secondary structures. This implementation of wriggling would ....

P. K. Weiner and P. A. Kollman, Amber: Assisted model building with energy refinement. a general program for modeling molecules and their interactions, Journal of Computational Chemistry 2 (1981) 287.

....it is possible to spend a considerable amount of time in a centralized strategy to come up with a good new mapping. 3 A scalable parallel algorithm for molecular dynamics Many existing implementations of parallel molecular dynamics use atom replication or atom decomposition techniques [1, 17]. Although these techniques allow relatively easy porting of existing sequential codes, they can be shown to be theoretically non scalable: as the number of processors increases, the communication to computation ratio also increases, even if the problem size is arbitrarily increased. More ....

P. K. Weiner and P. A. Kollman. AMBER: Assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981. 18

....of CHAOS that can be used to support efficient execution of irregular problems on distributed memory machines. This work was sponsored in part by ARPA (NAG 1 1485) and NSF (ASC 9213821) 1 Introduction Molecular dynamics (MD) simulation programs, such as CHARMM [1] GROMOS [2] and AMBER [3], are useful to study the structural, equilibrium, and dynamic properties of molecules. These programs are very complicated and computationally intensive. Implementing them on massively parallel processing systems not only reduces execution times but also allows users to solve larger problems. In ....

P. K. Weiner and P. A. Kollman. Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981.

....of CHAOS that can be used to support efficient execution of irregular problems on distributed memory machines. This work was sponsored in part by ARPA (NAG 1 1485) and NSF (ASC 9213821) 1 Introduction Molecular dynamics (MD) simulation programs, such as CHARMM [1] GROMOS [2] and AMBER [3], are useful to study the structural, equilibrium, and dynamic properties of molecules. These programs are very complicated and computationally intensive. Implementing them on massively parallel processing systems not only reduces execution times but also allows users to solve larger problems. In ....

P. K. Weiner and P. A. Kollman. Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981.

....capabilities, it is now generally acknowledged that the most feasible and economical means of solving extremely large computational problems in the future will be with highly parallel distributed memory architectures. The large molecular dynamics (MD) codes like CHARMM [3] GROMOS [10] AMBER [11], etc. have parts which are extremely computationally intensive. Implementationg these codes on massively parallel machines not only reduces the total solution time but allows one to solve very large problems. There are two software issues that needs to be addressed when one considers to ....

P. K. Weiner and P. A. Kollman, Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions, Journal of Computational Chemistry, 2 (1981), p. 287.

....before each computational phase. These problems are called irregular concurrent problems [9] Examples of irregular concurrent problems include adaptive and self adaptive explicit, multigrid unstructured computational fluid dynamic solvers [29, 15] molecular dynamics codes (CHARMM [5] AMBER [43], GROMOS [40] etc. diagonal or polynomial preconditioned iterative linear solvers [41] and time dependent flame modeling codes [32] This paper focuses on the runtime support, the language extensions, and the compiler support required to provide efficient data and work load distributions. The ....

P. K. Weiner and P. A. Kollman. Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981.

....the component, and OE 0 is the phase of the Fourier component. The number of components in the approximation depends on the type of the dihedral; improper dihedral angle an energy associated with improper dihedral angles can be used to enforce planarity of bonds around certain atoms. The AMBER [WK81] force field assigns an energy function similar to the one for normal dihedral angles. The CHARMM 1 [BBO 83] force field assigns to small improper dihedrals ( 6 ffi ) an energy similar to the one for angle bending. For larger angles CHARMM uses the same function as for dihedral angles. ....

.... entropy can be determined by examining the fluctuations of the structure around an energy minimum and computing the probability of the protein being in the particular minimum [VNS94] Several algorithms for the computation of entropy have been included in simulation programs like AMBER or CHARMM [WK81, BBO 83] 6 Disulfide bonds, hydrogen bonds, hydrophobicity Except for the interactions described in the previous section, several others affect the energy of proteins. The first interactions we describe in this section are the disulfide bonds. Disulfide bonds are covalent bonds that are ....

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Paul K. Weiner and Peter A. Kollman. Amber: Assisted model building with energy refining. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2(3):287--303, 1981.

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P. K. Weiner and P. A. Kollman, `Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions', Journal of Computational Chemistry, 2, 287 (1981).

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Weiner, P. K.; Kollman, P. A. AMBER: assisted model building with energy refinementA general program for modeling molecules and their interactions. J. Comput. Chem. 1981, 287-303.

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P. K. Weiner and P. A. Kollman. AMBER: Assisted model building with energy refinement. a general program for modeling molecules and their interactions. Journal of Computational Chemistry, 2:287, 1981. 9

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P. K. Weiner and P. A. Kollman, `Amber:assisted model building with energy refinement. a general program for modeling molecules and their interactions', Journal of Computational Chemistry, 2, 287, (1981).

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