B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, Swaminathan S., and M. Karplus. Charmm: A program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem., 4:187, 1983. Home/Search Document Not in Database Summary Related Articles Check |
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Improving Memory Hierarchy Performance for Irregular .. - Mellor-Crummey.. (2001) (6 citations) (Correct)
....the 8KB block size for the TLB is the amount of addressable memory in two pages associated with a TLB entry. 5.1. The Moldyn Benchmark Moldyn is a synthetic benchmark for molecular dynamics simulation. The computational structure in moldyn is similar to the nonbonded force calculation in CHARMM [33], and closely resembles the structure represented in Figure 1 of the paper. An interaction list is constructed for all pairs of interactions that are within a specified cutoff radius. These interactions are processed every timestep and are periodically updated due to particles changing their ....
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, S. Swaminathan, and M. Karplus, "CHARMM: A Program for Macromolecular Energy, Minimization and Dynamics Calculations," Journal of Computational Chemistry 187(4)(1983).
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....this plugin, the user can view the progress of the run graphically in addition to the usual view provided by Legion. Since special portals are merely more convenient interfaces to the basic functionality of initiating a run, creating new portals is simple. For example, a special portal for CHARMM [9] should take only a few hours to construct once the particulars of the application are available. Fig. 11. Special Portal for Amber 12 IV. SUPPORTED GRID SERVICES The Legion Grid Portal supports a significant subset of the capabilities and features of a grid system using Legion; the remaining ....
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., Karplus, M., "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comp. Chem., vol. 4, 1983.
Studying Protein Folding on the Grid: Experiences Using CHARMM.. - Le Gi On (Correct)
....available resources. In our experiment, a computational scientist accessed resources from NSF s National Partnership for Advanced Computational Infrastructure (NPACI) using the grid infrastructure provided by Legion. The application used was CHARMM (Chemistry at HARvard Molecular Mechanics) [3] [9] a popular general simulation package used by molecular biologists to study protein and nucleic acid structure and function. One large problem for which CHARMM is used is the study of the nature of the protein folding process. The scientist desired to study the energy and entropy of many ....
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., Karplus, M., "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comp. Chem., vol. 4, 1983.
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....and connection related metrics are given in the sequel. If weighted graphs are considered, node and edge numbers must be thought of as weights. 1. internal node number (subgraph) load balancing metric for applications with nodewise computations, for example molecular dynamics codes [1]. 2. internal edge number (subgraph) load balancing metric for applications with edgewise computations, for example Euler solvers [11] or matrix vector multiplication. 3. border node number (subgraph) communication metric for nodewise computations. 4. cut edge number (subgraph) ....
Brooks B. et al.: "CHARMM: A Program for Macromolecular Energy, Minimization and Dynamics Calculations", Computational Chemistry, Vol. 4, pp. 187-217, 1983.
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....As a result, many models have been developed using a classical description of molecules in terms of atomic bonds and effective interactions. Some of these parameterizations of molecular potential functions include ECEPP (Momany et al. 1975, 1974a,b) AMBER (Weiner et al. 1986, 1984) CHARMM (Brooks et al. 1983), DISCOVER (Dauber Osguthorpe et al. 1988) GROMOS (van Groningen and Berendsen, 1987) MM3 (Allinger et al. 1989) ENCAD (Levitt, 1983) ECEPP 2 (N emethy et al. 1983) and ECEPP 3 (N emethy et al. 1992) In general, these models, also known as force fields, are expressed as summations of ....
Brooks B., Bruccoleri R., Olafson B., States D., Swaminathan S., and Karplus M., 1983, Charmm: A program for macromolecular energy minimization and dynamics calculations.
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....interpreted to hand coded evaluation times can be August 22, 10 substantially larger than Tables 1 and 2 would suggest, particularly when the interpreted evaluation suffers many cache misses. We first illustrate this with a set of protein folding problems involving alanine polypeptides. See [3] for a description of the general protein folding objective function. Teresa Head Gordon kindly provided hand coded Fortran for this general objective and data for the particular alanine polypeptide problems; I modified the Fortran slightly to make joint computation of function and gradient more ....
B. R. BROOKS, R. E. BRUCCOLERI, B. D. OLAFSON, D. J. STATES, S. SWAMINATHAN, AND M. KARPLUS, "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations," J. Computational Chemistry 4 #2 (1983), pp. 187--217.
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....quantum mechanical ab initio calculations must be performed and used in combination with experimental results to effectively describe the molecular system. A number of empirically based molecular mechanics models have been developed for protein systems, including AMBER [74, 187, 188] CHARMM [19], DISCOVER [37] ECEPP [121, 122, 123] ECEPP 2 [130] ECEPP 3 [131] ENCAD [36, 103] GROMOS [175] MM2 [7] and MM3 [8, 106, 107] These models, also known as force fields, are typically expressed as summations of several potential energy components, with the mathematical form of individual ....
....costs of local minimizations and stochastic searching lead to large computational times. The concept of simulated annealing has also been applied to the area of molecular dynamics. Here the temperature is related to the kinetic energy, which can be obtained from the velocities of the atoms [19, 103]. Therefore, molecular dynamics annealing is accomplished by scaling atomic velocities. At high temperatures the conformational space is totally accessible due to large atomic velocities. As temperature is decreased, local conformations are defined because atomic velocities have been restricted. ....
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, CHARMM : A program for macromolecular energy minimization and dynamics calculations, J. Comp. Chem., 4, (1983), 187-217.
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....the polymer and a set of parameters computed from experimental data or quantum mechanics calculations. The functional forms of the energy terms and their associated parameters is called a forcefield. In the present study, we are making use of the commercially available CHARMm forcefield [1], as well as forcefield parameters taken from Muller Plathe et al. 2] Molecular mechanics and molecular dynamics. Molecular mechanics is the procedure by which one locates local minima of energy. Molecular mechanics simply consists of a minimization routine (conjugate gradient, steepest descent, ....
Brooks, B.R.; Bruccoleri, R. E.; Olafson, B.D.; States, D.J.; Swaminathan, S. and Karplus, M. "CHARMm: A program for macromolecular energy, minimization and dynamics calculations", J. Comp. Chem. 1983, 4, 187.
Unknown - Self-citation (Karplus) (Correct)
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B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, Swaminathan S., and M. Karplus. Charmm: A program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem., 4:187, 1983.
Effective Energy Function for Proteins in Solution - Lazaridis, Karplus (1999) (5 citations) Self-citation (Karplus) (Correct)
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Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983; 4:187--217.
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....but they generally include both covalent and non covalent terms. Bond stretching, angle bending, out of plane distortions, and torsion angle settings are the basic covalent terms and van der Waals interactions, electrostatic interactions, and hydrogen bonds are the basic non covalent terms. CHARMM [13], AMBER [97] and ENCAD [47] are three of the most common physics based potentials. Their main di erences are in the parameterization of the potential energy terms. CHARMM derives parameter values from a combination of ab initio calculations and empirical observation of protein structures. ENCAD ....
B.R. Brooks, R.E. Bruccoleri, B.D. Olafson, D.J. States, Swaminathan S., and M. Karplus. Charmm: A program for macromolecular energy minimization and dynamics calculations. J. Comp. Chem., 4:187, 1983.
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....available resources. In our experiment, a computational scientist accessed resources from NSF s National Partnership for Advanced Computational Infrastructure (NPACI) using the grid infrastructure provided by Legion. The application used was CHARMM (Chemistry at HARvard Molecular Mechanics) [3] [9] a popular general simulation package used by molecular biologists to study protein and nucleic acid structure and function. One large problem for which CHARMM is used is the study of the nature of the protein folding process. The scientist desired to study the energy and entropy of many ....
Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., Karplus, M., "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations", J. Comp. Chem., vol. 4, 1983.
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B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus, "CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations," Comp. Chem., no. 4, pp. 87--217, 1983.
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B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. Charmm: A program for macromolecular energy minimization, and dynamics calculations. J. Comput. Chem., 4:187--217, 1983.
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Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983;4: 187--217.
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Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983;4: 187--217.
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Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. CHARMM: a program for macromolecular energy minimization and dynamics calculations. J Comput Chem 1983; 4:187--217.
Runtime and Language Support for Compiling Adaptive.. - Hwang, Moon, Sharma (1995) (25 citations) (Correct)
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B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan and M. Karplus, `Charmm: A program for macromolecular energy, minimization, and dynamics calculations', Journal of Computational Chemistry, 4, 187 (1983).
BioCoRE: A Collaboratory for Structural Biology - Bhandarkar, Budescu.. (1999) (Correct)
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J. Mol. Biol., 112, 535--542. Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., and Karplus, M. 1983. CHARMM: A Program for Macromolecular Energy Minimization, and Dynamics Calculations.
Runtime and Language Support for Compiling Adaptive.. - Hwang, Moon, Sharma (1995) (25 citations) (Correct)
No context found.
B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, `Charmm: A program for macromolecular energy, minimization, and dynamics calculations', Journal of Computational Chemistry, 4, 187, (1983).
PASSION: Parallel And Scalable Software for Input-Output - Choudhary, Bordawekar.. (1994) (37 citations) (Correct)
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B. Brooks, R. Bruccoleri, B. Olafson, D. States, S. Swaminathan, and M. Karplus. CHARMM: A Program for Macromolecular Energy Minimization and Dynamic Calculations. Journal of Computational Chemistry, 4:187, 1983.
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