Coarse-grained molecular models for high-throughput and multi-scale functional investigations
نویسندگان
چکیده
منابع مشابه
Coarse-grained molecular models for high-throughput and multi-scale functional investigations
c © 2008 by John von Neumann Institute for Computing Permission to make digital or hard copies of portions of this work for personal or classroom use is granted provided that the copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. To copy otherwise requires prior specific permission by the publisher ment...
متن کاملCoarse-Grained Models Reveal Functional Dynamics – II. Molecular Dynamics Simulation at the Coarse-Grained Level – Theories and Biological Applications
Molecular dynamics (MD) simulation has remained the most indispensable tool in studying equilibrium/non-equilibrium conformational dynamics since its advent 30 years ago. With advances in spectroscopy accompanying solved biocomplexes in growing sizes, sampling their dynamics that occur at biologically interesting spatial/temporal scales becomes computationally intractable; this motivated the us...
متن کاملA coarse-grained model for a nanometer-scale molecular pump.
A theory for a nanometer-scale pump based on the ratchet concept is presented. A lattice gas model with a set of moves that satisfy hydrodynamic equations is used to describe an asymmetric nanometer channel connecting two reservoirs of fluid. The channel, which is coupled to an external oscillatory (or stochastic) driving force, pumps fluid from one reservoir to the other. The frequency of the ...
متن کاملESPResSo 3.1: Molecular Dynamics Software for Coarse-Grained Models
ESPRESSO is a package for Molecular Dynamics (MD) simulations of coarse-grained models. We present the most recent version 3.1 of our software, highlighting some recent algorithmic extensions to version 1.0 presented in a previous paper (Limbach et al. Comput Phys Commun 174:704–727, 2006). A major strength of our package is the multitude of implemented methods for calculating Coulomb and dipol...
متن کاملYUP: A Molecular Simulation Program for Coarse-Grained and Multi-Scaled Models.
Coarse-grained models can be very different from all-atom models and are highly varied. Each class of model is assembled very differently and some models need customized versions of the standard molecular mechanics methods. The most flexible way to meet these diverse needs is to provide access to internal data structures and a programming language to manipulate these structures. We have created...
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: Chemistry Central Journal
سال: 2008
ISSN: 1752-153X
DOI: 10.1186/1752-153x-2-s1-s14