Xiangda Peng

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The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit(More)
Cognition and memory impairment are hallmarks of the pathological cascade of various neurodegenerative disorders. Herein, we developed a novel computational strategy with two-dimensional virtual screening for not only affinity but also specificity. We integrated the two-dimensional virtual screening with ligand screening for 3D shape, electrostatic(More)
Classical molecular dynamic (MD) simulation of membrane proteins faces significant challenges in accurately reproducing and predicting experimental observables such as ion conductance and permeability due to its incapability of precisely describing the electronic interactions in heterogeneous systems. In this work, the free energy profiles of K(+) and Na(+)(More)
Center for Molecular Medicine, School of University of Technology, Dalian, 116023 foxmail.com Laboratory of Molecular Modeling and De Reaction Dynamics, Dalian Institute of C Sciences, 457 Zhongshan Rd., Dalian 11602 Department of Life Science and Bioph University, Shenyang 110016, P. R. China. E State Key Laboratory of Electroanalytical C Chemistry,(More)
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