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  • 1
    Electronic Resource
    Electronic Resource
    HIV-1 Protease Cleavage Mechanism Elucidated with Molecular Dynamics Simulation (1995)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 117 (1995), S. 5561-5572 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00125a018
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  • 2
    Electronic Resource
    Electronic Resource
    Constant pressure molecular dynamics simulation: The Langevin piston method (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 4613-4621 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A new method for performing molecular dynamics simulations under constant pressure is presented. In the method, which is based on the extended system formalism introduced by Andersen, the deterministic equations of motion for the piston degree of freedom are replaced by a Langevin equation; a suitable choice of collision frequency then eliminates the unphysical "ringing'' of the volume associated with the piston mass. In this way it is similar to the "weak coupling algorithm'' developed by Berendsen and co-workers to perform molecular dynamics simulation without piston mass effects. It is shown, however, that the weak coupling algorithm induces artifacts into the simulation which can be quite severe for inhomogeneous systems such as aqueous biopolymers or liquid/liquid interfaces.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.470648
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  • 3
    Electronic Resource
    Electronic Resource
    Three isomers of the aluminum-acetylene system (1979)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 101 (1979), S. 1638-1639 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00500a067
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  • 4
    Electronic Resource
    Electronic Resource
    Sudden polarization: pyramidalization of twisted ethylene (1979)
    s.l. : American Chemical Society
    Journal of the American Chemical Society 101 (1979), S. 307-311 
    Details
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/ja00496a005
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  • 5
    Electronic Resource
    Electronic Resource
    Solvent-Induced Forces between Two Hydrophilic Groups (1994)
    s.l. : American Chemical Society
    The @journal of physical chemistry 〈Washington, DC〉 98 (1994), S. 2198-2202 
    Details
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1021/j100059a038
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  • 6
    Electronic Resource
    Electronic Resource
    Computer simulation of liquid/liquid interfaces. I. Theory and application to octane/water (1995)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 103 (1995), S. 10252-10266 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: Statistical ensembles for simulating liquid interfaces at constant pressure and/or surface tension are examined, and equations of motion for molecular dynamics are obtained by various extensions of the Andersen extended system approach. Valid ensembles include: constant normal pressure and surface area; constant tangential pressure and length normal to the interface; constant volume and surface tension; and constant normal pressure and surface tension. Simulations at 293 K and 1 atm normal pressure show consistent results with each other and with a simulation carried out at constant volume and energy. Calculated surface tensions for octane/water (61.5 dyn/cm), octane/vacuum (20.4 dyn/cm) and water/vacuum (70.2 dyn/cm) are in very good agreement with experiment (51.6, 21.7, and 72.8 dyn/cm, respectively). The practical consequences of simulating with two other approaches commonly used for isotropic systems are demonstrated on octane/water: applying equal normal and tangential pressures leads to an instability; and applying a constant isotropic pressure of 1 atm leads to a large positive normal pressure. Both results are expected for a system of nonzero surface tension. Mass density and water polarization profiles in the liquid/liquid and liquid/vapor interfaces are also compared.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.469927
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  • 7
    Electronic Resource
    Electronic Resource
    Removal of pressure and free energy artifacts in charged periodic systems via net charge corrections to the Ewald potential (1998)
    College Park, Md. : American Institute of Physics (AIP)
    The Journal of Chemical Physics 108 (1998), S. 7070-7084 
    Details
    ISSN: 1089-7690
    Source: AIP Digital Archive
    Topics: Physics , Chemistry and Pharmacology
    Notes: A uniform neutralizing background plasma is employed by default in standard Ewald calculations for net-charged systems. We show here that this plasma leads to serious artifacts in both system energy and pressure, which lead to unrealistic behavior. These artifacts are especially critical to simulations where either net charge or volume is allowed to change. To correct these problems we institute a net-charge correction term that consists of subtracting off the Ewald sum for a single particle with charge equal to the net charge of the full system and an optional Born or Poisson–Boltzmann term. This correction decreases pressure artifacts by three orders of magnitude and allows rapid energy convergence as the cell size increases. The correction term is general, in that it applies to systems of any shape or net charge. The net-charge correction was tested for systems in all three phases of matter: gas, solid, and liquid, and found to be markedly superior to standard Ewald in all three cases. In the gas phase, isolated molecular energies are quickly achieved as the cell size increases. In the solid phase the vaporization energy of the NaCl crystal is reproduced using free energy perturbation techniques where a single atom is removed. In the liquid phase, the solvation free energy of Na+ was investigated. It is demonstrated that both the net-charge correction and an energy term twice the size of a Born term is required to obtain optimal free energies of ionic hydration. © 1998 American Institute of Physics.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.476320
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  • 8
    Electronic Resource
    Electronic Resource
    Recent advances in molecular dynamics simulation towards the realistic representation of biomolecules in solution (1998)
    Springer
    Theoretical chemistry accounts 99 (1998), S. 279-288 
    Details
    ISSN: 1432-2234
    Keywords: Key words: Molecular dynamics ; Biomolecular simulation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Abstract. Coupled advances in empirical force fields and classical molecular dynamics simulation methodologies, combined with the availability of faster computers, has lead to significant progress towards accurately representing the structure and dynamics of biomolecular systems, such as proteins, nucleic acids, and lipids in their native environments. Thanks to these advances, simulation results are moving beyond merely evaluating force fields, displaying expected structural fluctuations, or demonstrating low root-mean-squared deviations from experimental structures and now provide believable structural insight into a variety of processes such as the stabilization of A-DNA in mixed water and ethanol solution or reversible β-peptide folding in methanol. The purpose of this overview is to take stock of these recent advances in biomolecular simulation and point out some common deficiencies exposed in longer simulations. The most significant methodological advances relate to the development of fast methods to properly treat long-range electrostatic interactions, and in this regard the fast Ewald methods are becoming the de facto standard.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002140050337
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  • 9
    Electronic Resource
    Electronic Resource
    The effects of truncating long-range forces on protein dynamics (1989)
    New York, NY : Wiley-Blackwell
    Proteins: Structure, Function, and Genetics 6 (1989), S. 32-45 
    Details
    ISSN: 0887-3585
    Keywords: long range truncation ; molecular dynamics ; myoglobin ; truncation effects ; protein electrostatics ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Medicine
    Notes: This paper considers the effects of truncating long-range forces on protein dynamics. Six methods of truncation that we investigate as a function of cutoff criterion of the long-range potentials are (1) a shifted potential; (2) a switching function; (3) simple atom-atom truncation based on distance; (4) simple atom-atom truncation based on a list which is updated periodically (every 25 steps); (5) simple group-group truncation based on distance; and (6) simple group-group truncation based on a list which is updated periodically (every 25 steps). Based on 70 calculations of carboxymyoglobin we show that the method and distance of long range cutoff have a dramatic effect on overall protein behavior. Evaluation of the different methods is based on comparison of a simulation's rms fluctuation about the average coordinates of a no cutoff simulation and from the X-ray structure of the protein. The simulations in which long-range forces are truncated by a shifted potential shows large rms deviations for cutoff criteria less than 14 Å, and reasonable deviations and fluctuations at this cutoff distance or larger. Simulations using a switching function are investigated by varying the range over which electrostatic interactions are switched off. Results using a short switching function that switches off the potential over a short range of distances are poor for all cutoff distances. A switching function over a 5-9 Å range gives reasonable results for a distance-dependent dielectric, but not using a constant dielectric. Both the atom-atom and group-group truncation methods based on distance shows large rms deviations and fluctuation for short cutoff distance, while for cutoff distance of 11 Å or greater, reasonable results are achieved. Although comparison of these to distance-based truncation methods show surprisingly larger rms deviations for the group-group truncation, contrary to simulation studies of aqueous ionic solutions. The results of atom-atom or group-group list-based simulations generally appear to be less stable than the distance-based simulations, and require more frequent velocity scaling or stronger coupling to a heat bath.
    Additional Material: 7 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/prot.340060104
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  • 10
    Electronic Resource
    Electronic Resource
    The BERKELEY system. III. General configuration-interaction methods for open-shell molecular electronic states (1978)
    New York, NY : Wiley-Blackwell
    International Journal of Quantum Chemistry 14 (1978), S. 603-612 
    Details
    ISSN: 0020-7608
    Keywords: Computational Chemistry and Molecular Modeling ; Atomic, Molecular and Optical Physics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A system of general “open-ended” configuration-interaction (CI) programs, specifically designed for the Harris Corporation Slash Four minicomputer, is described. These methods are general in the sense that an arbitrary list of configurations (linear combinations of Slater determinants) may be used, and open ended in that peripheral (i.e., disk) storage capacity determines the maximum size problem that can be solved. The largest variational calculations carried out to date using BERKELEY involve 7064 open-shell singlet configurations (31,898 Slater determinants). Detailed timing breakdowns are presented for four test cases, two of which involve the lowest ππ* singlet state of ethylene. The other two examples are the orthogonal or bisected singlet state of trimethylenemethane and the 8B1 state of the MnCH2 complex. In the latter case, it is found that the predicted Mn—CH2 dissociation energy is only slightly increased by electron correlation effects.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/qua.560140507
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