B. R. Brooks et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. of Computational Chemistry, (4):187--217, 1983. Home/Search Document Not in Database Summary Related Articles Check |
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Expert Antibody Side Chain Placement - Ritchie (Correct)
....is the Dead End Elimination (DEE) algorithm of Desmet et al. 10] This also makes use of a rotamer library but in a somewhat novel way. The basic principle is to eliminate candidate rotamers The Protein Data Bank [2] at Brookhaven is one of the main protein structure libraries. CHARMM [4] is the molecular dynamics module of the QUANTA package. 18 on energetic considerations. All energy based approaches attempt to solve for the minimum energy conformation of the system. In terms of rotamer search, Desmet calls this the global minimum energy conformation (GMEC) The basic DEE ....
Brooks B.R., Bruccoleri R.E., Olafson B.D., States D.J., Swaminathan S., Karplus M. (1983), CHARMM: A program for macromolecular energy, minimisation and dynamics calculations, J. Comput. Chem. 4 187--217.
On the Automatic Parallelization of Sparse and.. - Asenjo, Eladio.. (1997) (5 citations) (Correct)
....enddo enddo Here indirection occurs on the right hand side of the computed expressions. The matrix BCSSTK14 from the Harwell Boeing collection has been used as input to this benchmark. 2. 7 NBFC The calculation of non bonded forces forms a key element of many molecular dynamics computations [8]. NBFC computes an electro static interaction between particles where the forces acting on an atom are calculated from a list of neighboring atoms. Similar to the DSMC3D benchmark, the data access pattern in this sparse code has indirection on both sides of the computed expressions: do k = 1, ....
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., 4:187--217, 1983.
A Test Set for Molecular Dynamics Algorithms - Barth, Leimkuhler, Reich (2002) (Correct)
....has been ongoing [29 31] The many parameters b , OE , and equilibrium values b , OE , in table 1 are determined empirically for interactions involving each possible combination of atoms. Many potential parameterizations are available, including CHARMM [32,33], AMBER [34,35] and OPLS [36] A list of references to these and other MD potentials can be found in [37] The MD potential is highly nonlinear, with many local minima. Minimization of the potential energy is a common task, but the nonpolynomial proliferation of local minima frustrates attempts ....
.... CH3 CH2 CH2 CH3 OE = 1:6 kcal mol, OE = 0:0 , n OE = 3 Lennard Jones CH3 ffl = 0:1811 kcal mol, oe = 2:165 A A small flexible molecule A frequently used test problem in molecular dynamics simulation is the so called alanine dipeptide (more properly NAcetylalanyl N Methylamide) [32,47,97,98]. Small in size (22 atoms) alanine dipeptide is a good model system because it exhibits conformational flexibility in the 2 dimensional OE Gamma dihedral space. The dihedral angles OE and are illustrated in Fig. 5. The changes in structure seen through the dynamics of the backbone dihedral ....
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), pp. 187-- 217
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 ....
....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 ....
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., 4:187--217, 1983.
Combining Task- and Data Parallelism to Speed up.. - Uk, Taufer.. (2003) (Correct)
....data parallelism for a specific protein, the GSGS domain. In Section 6, we summarize what we learned from our experiment and conclude. 2. PROTEIN FOLDING 2. 1 The Computational Code CHARMM CHARMM is a code for simulating the structure of biologically relevant macromolecules (proteins, DNA, RNA) [10]. The package uses classical mechanical methods to investigate potential energy surfaces derived from experimental and ab initio quantum chemical calculations [11] We use molecular dynamics (MD) simulations at constant temperature to investigate the protein folding process. In these simulations ....
....3.1.2 Benefits of more accurate calculation models For the folding of small proteins and structured peptides, which naturally occurs in the stomstimescale,several models are being used. We will focus our attention on the empirical models with implicit or explicit treatment of solvent [10, 17]. In the implicit solvent models, all atoms of the solute are taken into account, while the e#ects of solvent (charge screening, free energy of solvation etc. are approximated with expressions that depend on the coordinates of the solute atoms [18] The main advantage of this approach consists of ....
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.
Study of a Highly Accurate and Fast Protein-Ligand Docking.. - Based On Molecular Self-citation (Brooks) (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. J. Comput. Chem., 4:187--217, 1983.
Study of a Highly Accurate and Fast Protein-Ligand Docking.. - Based On Molecular (2004) Self-citation (Brooks) (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. J. Comput. Chem., 4:187--217, 1983.
Protein Sidechain Conformer Prediction: A Test of the.. - Petrella, Lazaridis.. (1998) (1 citation) Self-citation (Karplus) (Correct)
.... does a full, rigid rotation search for the remaining sidechain lead to an energy map with the correct minimum energy conformation Such a minimal test was made for the bovine pancreatic trypsin inhibitor (BPTI) when the energy function used in an early version of what is now the CHARMM program [40] was first introduced [34] It was found that varying one sidechain angle at a time, 27 out of a total of 36 sidechains were well predicted (42 out of 58 dihedral angles, or 72.4 , correct in this group) and nine residues were poorly predicted (10 of 37 angles, or 27.0 , correct) where the ....
....crystal orientation corresponded to the absolute minimum of the complete (i.e. continuous) energy map for a given residue, a 10 grid was successful in locating it 99.7 of the time. Calculations of the torsional energies were carried out using a standard CHARMM empirical potential energy function [40]. Version 19 of parameter and topology files was used [42] which defines a polar hydrogen protein model, with non polar hydrogens represented by extended atoms. Because all except the chosen dihedral angles of one sidechain remain unchanged during the rigid geometry mapping procedure, the energy ....
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Brooks, B.R., et al., & Karplus, M. (1983). CHARMM: a program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187.
Parallelizing Molecular Dynamics Programs for.. - Hwang, Das, Saltz.. (1994) (25 citations) Self-citation (Brooks) (Correct)
....paper presents an application 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 ....
....are presented in Section 7. 2 Molecular Dynamics (CHARMM) CHARMM is a program which calculates empirical energy functions to model macromolecular systems. The purpose of CHARMM is to derive structural and dynamic properties of molecules using the first and second order derivative techniques [1]. The computationally intensive part of CHARMM is the molecular dynamics simulation. This calculation is usually performed when the molecular structure reaches a local stable state (low energy) through energy minimization. It simulates the dynamic interactions among all atoms in the system for a ....
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.
SmartApps, an Application Centric Approach to High .. - Dang, Garzaran.. (Correct)
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B. R. Brooks et al. CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. of Computational Chemistry, (4):187--217, 1983.
Exploring Phase-Transfer Catalysis with Molecular.. -.. (2005) (Correct)
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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. Comput. Chem. 1983, 4, 187-217.
Mdsimaid: An Automatic Recommender For Optimization Of Fast.. - Ko (2002) (3 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, minmimization, and dynamics calculations. J. Comp. Chem, 4, 1983.
Polarizable Force Fields For Flexible Molecules - Holt (2004) (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. J. Comp. Chem., 4(2):187--217, 1983.
Development of Molecular Dynamics Simulation System for.. - Ishida, Joti, al. (2003) (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, J. Comp. Chem. 4, 187--217 (1983).
Protein Sequence Optimization - Theory, Practice, and Fundamental.. - Torda (2004) (Correct)
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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. Comput. Chem. 1983, 4, 187 -- 217.
On the Automatic Parallelization of Sparse and.. - Asenjo.. (1997) (5 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. J. Comp. Chem., 4:187--217, 1983.
Theory, Techniques, and Experiments in Solving Recurrences in.. - Pottenger (1997) (1 citation) (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. J. Comp. Chem., 4:187--217, 1983.
Theory, Techniques, And Experiments In Solving Recurrences In.. - Pottenger (1997) (1 citation) (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. J. Comp. Chem.,4:1? 1983.
From Legion to Legion-G to OGSI.NET: Object-based.. - Marty Humphrey.. (Correct)
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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, Journal of Computational Chemistry, Vol. 4, 1983.
Theory, Techniques, and Experiments in Solving Recurrences in.. - Pottenger (1997) (1 citation) (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. J. Comp. Chem., 4:187--217, 1983.
NAMD User's Guide - Version 2.5 - Bhandarkar, Brunner, Chipot, Dalke.. (2003) (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. J. Comp. Chem., 4(2):187--217, 1983.
A Constraint-Based Approach for Deriving 3-D Structures of Cyclic .. - Rodosek (Correct)
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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 Dynamic Calculations, " Journal of Computational Chemistry 4(2), 1983, pp. 187 - 217.
Effective Energy Functions for Protein Structure Prediction - Lazaridis, 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.
A Tutorial to Set up Alchemical Free Energy Perturbation.. - Dixit, Henin, Chipot (2004) (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. J. Comput. Chem., 4:187--217, 1983.
Automatic Differentiation Bibliography - Corliss (1992) (1 citation) (Correct)
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B. R. BROOKS, R. E. BRVCCOLERI, B. D. OLAfSON, D. J. STATES, S. SWAMINATHAN, AND M. KARPLUS, CHARMM: A program for macromolecular energy, min- imization, and dynamics calculations, J. Computational Chemistry, 4 (1983), pp. 187- 217.
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