Driven Molecular Dynamics for Normal Modes of Biomolecules without the Hessian, and Beyond

Author(s):  
Alex Brown ◽  
Martina Kaledin ◽  
Joel Bowman ◽  
Alexey Kaledin
Proteins ◽  
1991 ◽  
pp. 220-228 ◽  
Author(s):  
Martha M. Teeter ◽  
Usha Rao ◽  
David Case

2019 ◽  
Vol 04 (02) ◽  
pp. 1950002 ◽  
Author(s):  
Ivan P. Lobzenko

Properties of discrete breathers are discussed from two points of view: (I) the ab initio modeling in graphene and (II) classical molecular dynamics simulations in the ace-centered cubic (fcc) Ni. In the first (I) approach, the possibility of exciting breathers depends on the strain applied to the graphene sheet. The uniaxial strain leads to opening the gap in the phonon band and, therefore, the existence of breathers with frequencies within the gap. In the second (II) approach, the structure of fcc Ni supports breathers of another kind, which possess a hard nonlinearity type. It is shown that particular high frequency normal mode can be used to construct the breather by means of overlaying a spherically symmetrical function, the maximum of which coincides with the breather core. The approach of breathers excitation based on nonlinear normal modes is independent of the level of approximation. Even though breathers could be obtained both in classical and first-principles calculations, each case has advantages and shortcomings, that are compared in the present work.


Author(s):  
Asegun S. Henry ◽  
Gang Chen

Silicon's material properties, have been studied extensively because of its technological significance in a variety of industries, including microelectronics. Yet, questions surrounding the phonon relaxation times in silicon continue to linger.1,2 Previous theoretical works3-5 have generated qualitative expressions for phonon relaxation times, however these approaches require fitting parameters that cannot be determined reliably. This paper first discusses implementation issues associated with using the Green-Kubo method in molecular dynamics (MD) simulations. We compare various techniques used in similar works and discusses several implementation issues that have arisen in the literature. We then describe an alternative procedure for analyzing the normal modes of a crystal to extract phonon relaxation times. As an example material we study bulk crystalline silicon using equilibrium MD simulations and lattice dynamics. The environment dependent interatomic potential6 is used to model the interactions and frequency dependent phonon properties are extracted from the MD simulations.


2003 ◽  
Vol 107 (46) ◽  
pp. 12820-12828 ◽  
Author(s):  
Xin Yu ◽  
Jongsoon Park ◽  
David M. Leitner

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