Coarse-grained V representability
نویسندگان
چکیده
منابع مشابه
Representability problems for coarse-grained water potentials.
The use of an effective intermolecular potential often involves a compromise between more accurate, complex functional forms and more tractable simple representations. To study this choice in detail, we systematically derive coarse-grained isotropic pair potentials that accurately reproduce the oxygen-oxygen radial distribution function of the TIP4P-Ew water model at state points over density r...
متن کاملCoarse-Grained Simulation of Myosin-V Movement
We describe the development of a hierarchic modelling method applied to simulating the processive movement of the myosin-V molecular motor protein along an actin filament track. In the hierarchic model, three different levels of protein structure resolution are represented: secondary structure, domain, and protein, with the level of detail changing according to the degree of interaction among t...
متن کاملHigh-Resolution Coarse-Grained Modeling Using Oriented Coarse-Grained Sites.
We introduce a method to bring nearly atomistic resolution to coarse-grained models, and we apply the method to proteins. Using a small number of coarse-grained sites (about one per eight atoms) but assigning an independent three-dimensional orientation to each site, we preferentially integrate out stiff degrees of freedom (bond lengths and angles, as well as dihedral angles in rings) that are ...
متن کاملCoarse Grained Molecular Kinetics
The dynamic behavior of molecules can often be described by Markov processes. From computational molecular simulations one can derive transition rates or transition probabilities between subsets of the discretized conformational space. On the basis of this dynamic information, the spatial subsets are combined into a small number of so-called metastable molecular conformations. This is done by c...
متن کاملCoarse graining from coarse-grained descriptions.
We present a generalization of Zwanzig's method of projection operators to the case where the underlying dynamics is not deterministic. The method allows us to perform a coarse graining of an already coarse-grained level of description in which fluctuations are important. The initial level of description is described by a Fokker-Planck equation and, under suitable approximations, the final slow...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: The Journal of Chemical Physics
سال: 2006
ISSN: 0021-9606,1089-7690
DOI: 10.1063/1.2336211