We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures,...We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.展开更多
The stereodynamics of the reaction of Ca ＋ HCl are calculated at three different collision energies based on the potential energy surface [Verbockhaven G et al. 2005 J. Chem. Phys. 122 204307] using quasi-classical t...The stereodynamics of the reaction of Ca ＋ HCl are calculated at three different collision energies based on the potential energy surface [Verbockhaven G et al. 2005 J. Chem. Phys. 122 204307] using quasi-classical trajectory theory. The polarization-dependent differential cross sections （PDDCSs） （2π/σ ）（dσ 00 /dω t ）, （2π/σ ）（dσ 20 /dωt ）, （2π/σ ）（dσ 22＋ /dωt ）, （2π/σ ）（dσ 21 /dω t ） and the distributions of P（θ r ）, P（φr ）, and P（θr ,φr ） are calculated. The results indicate that the rotational polarization of the CaCl product presents different characteristics for the different collision energies, and the effects of the collision energy on the vector potential, including the alignment, orientation, and PDDCSs, are not obvious.展开更多
基金Supported by the National Natural Science Foundation of China under Grant Nos 31200545,11274206 and 11574184
文摘We report the results of protein folding （219M, C34, N36, 2KES, 2KHK） by the method of accelerated molecular dynamics （aMD） at room temperature with the implicit solvent model. Starting from the linear structures, these proteins successfully fold to the native structure in a lO0-ns aMD simulation. In contrast, they are failed under the traditional MD simulation in the same simulation time. Then we find that the lowest root mean square deviations of helix structures from the native structures are 0.36 A, 0.63 A, 0.52 A, 1.1 A and 0.78 A. What is more, native contacts, cluster and free energy analyses show that the results of the aMD method are in accordance with the experiment very well. All analyses show that the aMD can accelerate the simulation process, thus we may apply it to the field of computer aided drug designs.
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 11174117, 10974078, 11274205, 11274206, 11147026, and 31200545)
文摘The stereodynamics of the reaction of Ca ＋ HCl are calculated at three different collision energies based on the potential energy surface [Verbockhaven G et al. 2005 J. Chem. Phys. 122 204307] using quasi-classical trajectory theory. The polarization-dependent differential cross sections （PDDCSs） （2π/σ ）（dσ 00 /dω t ）, （2π/σ ）（dσ 20 /dωt ）, （2π/σ ）（dσ 22＋ /dωt ）, （2π/σ ）（dσ 21 /dω t ） and the distributions of P（θ r ）, P（φr ）, and P（θr ,φr ） are calculated. The results indicate that the rotational polarization of the CaCl product presents different characteristics for the different collision energies, and the effects of the collision energy on the vector potential, including the alignment, orientation, and PDDCSs, are not obvious.
