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Jeffry D. Madura

Bio: Jeffry D. Madura is a academic researcher at Duquesne University who has co-authored 143 publication(s) receiving 38515 citation(s). The author has an hindex of 39. Previous affiliations of Jeffry D. Madura include National Center for Atmospheric Research & University of Pittsburgh. The author has done significant research in the topic(s): Docking (molecular) & Antifreeze protein.

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Papers
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Journal ArticleDOI: 10.1063/1.445869
Abstract: Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC, ST2, TIPS2, TIP3P, and TIP4P. Comparisons are made with experimental thermodynamic and structural data including the recent neutron diffraction results of Thiessen and Narten. The computed densities and potential energies are in reasonable accord with experiment except for the original BF model, which yields an 18% overestimate of the density and poor structural results. The TIPS2 and TIP4P potentials yield oxygen–oxygen partial structure functions in good agreement with the neutron diffraction results. The accord with the experimental OH and HH partial structure functions is poorer; however, the computed results for these functions are similar for all the potential functions. Consequently, the discrepancy may be due to the correction terms needed in processing the neutron data or to an effect uniformly neglected in the computations. Comparisons are also made for self‐diffusion coefficients obtained from molecular dynamics simulations. Overall, the SPC, ST2, TIPS2, and TIP4P models give reasonable structural and thermodynamic descriptions of liquid water and they should be useful in simulations of aqueous solutions. The simplicity of the SPC, TIPS2, and TIP4P functions is also attractive from a computational standpoint.

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Topics: Water model (53%), Solvent models (52%), Water dimer (51%) ...read more

29,424 Citations


Journal ArticleDOI: 10.1021/JA00334A030
Abstract: Optimized intermolecular potential functions have been determined for hydrocarbons through Monte Carlo simulations of 15 liquids: methane, ethane, propane, n-butane, isobutane, n-pentane, isopentane, neopentane, cyclopentane, n-hexane, 1-butene, cis- and trans-2-butene, isobutene, and benzene. To achieve high accuracy, 12 unique group types were identified and their associated Lennard-Jones parameters were established. The average deviation from experiment for the computed densities and heats of vaporization is 2% and trends for isomeric series are reproduced. Conformation results were also obtained for five liquids and revealed no condensed-phase effects on the conformer populations. Structural analyses focus on trends as a function of chain length and branching of the monomers.

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Topics: Isopentane (56%), Neopentane (56%), Pentane (55%) ...read more

1,907 Citations


Journal ArticleDOI: 10.1063/1.1683075
Abstract: A re-parameterization of the standard TIP4P water model for use with Ewald techniques is introduced, providing an overall global improvement in water properties relative to several popular nonpolarizable and polarizable water potentials. Using high precision simulations, and careful application of standard analytical corrections, we show that the new TIP4P-Ew potential has a density maximum at approximately 1 degrees C, and reproduces experimental bulk-densities and the enthalpy of vaporization, DeltaH(vap), from -37.5 to 127 degrees C at 1 atm with an absolute average error of less than 1%. Structural properties are in very good agreement with x-ray scattering intensities at temperatures between 0 and 77 degrees C and dynamical properties such as self-diffusion coefficient are in excellent agreement with experiment. The parameterization approach used can be easily generalized to rehabilitate any water force field using available experimental data over a range of thermodynamic points.

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Topics: Water model (53%)

1,504 Citations


Journal ArticleDOI: 10.1016/0010-4655(95)00043-F
Abstract: Brownian dynamics simulations are not new, but typically progrmas have been written for specific systems. In this paper, we describe a general-purpose Brownian dynamics program that has been developed at the University of Houston. The program can simulate the diffusion of flexible chains. The rates of diffusion-controlled reactions can be calculated for arbitrary reaction geometries. Electrostatic interactions among the diffusing species are modeled by the use of finite difference solutions of the linearized Poisson-Boltzmann equation. The program can also be used for electrostatic force and energy calculations. Provisions are made for coordinate and parameter manipulations. The basic structure of the program and its functionality are discussed and some example applications are cited.

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Topics: Brownian dynamics (60%), Brownian motion (51%)

891 Citations


Journal ArticleDOI: 10.1080/00268978500103111
20 Dec 1985-Molecular Physics
Abstract: A series of Monte Carlo simulations has been carried out to characterize the temperature and size dependence of the results for liquid water using the TIP4P potential function. Five temperatures from -25 to 100°C and four system sizes from 64 to 512 molecules have been studied. Comparisons are made with experimental thermodynamic and structural data as well as results of prior simulations.

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680 Citations


Cited by
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Open access
Steven J. Plimpton1Institutions (1)
01 May 1993-
Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

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Topics: Intel Paragon (64%), Intel iPSC (62%), Parallel algorithm (58%)

24,496 Citations


Journal ArticleDOI: 10.1063/1.470117
Ulrich Essmann1, Lalith Perera1, Max L. Berkowitz, Tom Darden2  +2 moreInstitutions (2)
Abstract: The previously developed particle mesh Ewald method is reformulated in terms of efficient B‐spline interpolation of the structure factors This reformulation allows a natural extension of the method to potentials of the form 1/rp with p≥1 Furthermore, efficient calculation of the virial tensor follows Use of B‐splines in place of Lagrange interpolation leads to analytic gradients as well as a significant improvement in the accuracy We demonstrate that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N) For biomolecular systems with many thousands of atoms this method permits the use of Ewald summation at a computational cost comparable to that of a simple truncation method of 10 A or less

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Topics: P3M (68%), Ewald summation (66%), Particle Mesh (56%) ...read more

15,288 Citations


Open accessJournal ArticleDOI: 10.1021/CT700301Q
Abstract: Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions Not only does this combination of a

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  • Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
    Figure 5. Performance for lysozyme in water (24119 atoms) with OPLS-aa and PME on a 3 GHz dual core Intel Core2 cluster with 2 (solid lines) and 4 (dashed lines) cores per InFIniband interconnect. The dot-dashed line indicates linear scaling.
  • Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
    Table 3. Number of Steps per Second for a Coarse-Grained Polystyrene Modela
  • Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
    Table 1. Number of MD Steps per Second with and without Spatial Sorting of Charge Groupsa
  • Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
    Table 5. Simulation Speed in ns/day with GROMACS 4 Domain Decomposition and GROMACS 3.3 Particle Decomposition for the Membrane/Protein System (121449 Atoms)a
  • Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
    Table 4. Parameters for the DHFR Benchmark and the Energy Drift per Degree of Freedom
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Topics: Particle Mesh (50%)

12,609 Citations


Journal ArticleDOI: 10.1021/JP973084F
Abstract: New protein parameters are reported for the all-atom empirical energy function in the CHARMM program. The parameter evaluation was based on a self-consistent approach designed to achieve a balance between the internal (bonding) and interaction (nonbonding) terms of the force field and among the solvent−solvent, solvent−solute, and solute−solute interactions. Optimization of the internal parameters used experimental gas-phase geometries, vibrational spectra, and torsional energy surfaces supplemented with ab initio results. The peptide backbone bonding parameters were optimized with respect to data for N-methylacetamide and the alanine dipeptide. The interaction parameters, particularly the atomic charges, were determined by fitting ab initio interaction energies and geometries of complexes between water and model compounds that represented the backbone and the various side chains. In addition, dipole moments, experimental heats and free energies of vaporization, solvation and sublimation, molecular volume...

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Topics: Ab initio (59%), Force field (chemistry) (53%), Solvation (53%) ...read more

12,333 Citations


Journal ArticleDOI: 10.1021/CR9904009
26 Jul 2005-Chemical Reviews
Abstract: 6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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11,599 Citations


Performance
Metrics

Author's H-index: 39

No. of papers from the Author in previous years
YearPapers
20201
20183
20176
20166
20154
20146

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Author's top 5 most impactful journals

Biophysical Journal

9 papers, 377 citations

Proteins

7 papers, 250 citations

Journal of Physical Chemistry B

7 papers, 215 citations

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