Browsing by Author "Zhang, Cheng"

Now showing 1 - 4 of 4
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    Enhanced sampling and applications in protein folding
    (2013-07-24) Zhang, Cheng; Ma, Jianpeng; McNew, James A.; Igoshin, Oleg A.
    We show that a single-copy tempering method is useful in protein-folding simulations of large scale and high accuracy (explicit solvent, atomic representation, and physics-based potential). The method uses a runtime estimate of the average potential energy from an integral identity to guide a random walk in the continuous temperature space. It was used for folding three mini-proteins, trpzip2 (PDB ID: 1LE1), trp-cage (1L2Y), and villin headpiece (1VII) within atomic accuracy. Further, using a modification of the method with a dihedral bias potential added on the roof temperature, we were able to fold four larger helical proteins: α3D (2A3D), α3W (1LQ7), Fap1-NRα (2KUB) and S-836 (2JUA). We also discuss how to optimally use simulation data through an integral identity. With the help of a general mean force formula, the identity makes better use of data collected in a molecular dynamics simulation and is more accurate and precise than the common histogram approach.
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    Enhanced sampling method for free energy calculation and large scale conformational change
    (2009) Zhang, Cheng
    A method of directly computing the partition function (or the corresponding free energy) and accelerating configurational sampling is developed. In an expanded ensemble, the method can quickly sample a broad distribution and yield accurate results for the partition function. The method is shown to be efficient and accurate in studying thermodynamic properties, searching low-energy configurations of difficult molecular systems and counting solutions of puzzles.
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    Estimating statistical distributions using an integral identity
    (American Institute of Physics, 2012) Zhang, Cheng; Ma, Jianpeng; Applied Physics Program
    We present an identity for an unbiased estimate of a general statistical distribution. The identity computes the distribution density from dividing a histogram sum over a local window by a correction factor from a mean-force integral, and the mean force can be evaluated as a configuration average. We show that the optimal window size is roughly the inverse of the local mean-force fluctuation. The new identity offers a more robust and precise estimate than a previous one by Adib and Jarzynski [J. Chem. Phys. 122, 014114 (2005)]10.1063/1.1829631. It also allows a straightforward generalization to an arbitrary ensemble and a joint distribution of multiple variables. Particularly we derive a mean-force enhanced version of the weighted histogram analysis method. The method can be used to improve distributions computed from molecular simulations. We illustrate the use in computing a potential energy distribution, a volume distribution in a constant-pressure ensemble, a radial distribution function, and a joint distribution of amino acid backbone dihedral angles.
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    Multicanonical molecular dynamics by variable-temperature thermostats and variable-pressure barostats
    (American Institute of Physics, 2013) Zhang, Cheng; Deem, Michael W.
    Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics. These methods use a variable temperature or pressure that is updated on the fly in the thermodynamic controller. These methods are illustrated on a Lennard-Jones system and a structure-based model of proteins.