Conditional reversible work method for molecular coarse graining applications.
نویسندگان
چکیده
Systematically coarse grained models for complex fluids usually lack chemical and thermodynamic transferability. Efforts to improve transferability require the development of effective potentials with unequivocal physical significance. In this paper, we introduce conditional reversible work (CRW) potentials that describe nonbonded interactions in coarse grained models at the pair level. The method used to obtain these potentials is straightforward to implement, can be readily extended to compute hydration contributions in implicit-solvent potentials, and is easy to automize. As a first illustration of the method, we present CRW potentials for 3-site models of hexane and toluene. The temperature-transferability of the liquid phase density obtained with these potentials has been investigated, and a comparison has been made with effective potentials obtained by the iterative Boltzmann inversion method.
منابع مشابه
Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.
Coarse-graining of atomistic force fields allows us to investigate complex biological problems, occurring at long timescales and large length scales. In this work, we have developed an accurate coarse-grained model for double-stranded DNA chain, derived systematically from atomistic simulations. Our approach is based on matching correlators obtained from atomistic and coarse-grained simulations...
متن کاملEnhanced Coarse-Graining of Thermoplastic Polyurethane Elastomer for Multiscale Modeling
The objective of this work is to develop a multiscale modeling tool of copolymers with long chains. We propose an enhanced coarse-graining method of thermoplastic polyurethane (TPU) with three beads. The proposed coarse-graining provides an accurate molecular modeling tool to keep the molecular interaction together with computational efficiency. The coarse-grained model with three beads is furt...
متن کاملA coarse-graining approach for molecular simulation that retains the dynamics of the all-atom reference system by implementing hydrodynamic interactions.
We report on a new approach for deriving coarse-grained intermolecular forces that retains the frictional contribution that is often discarded by conventional coarse-graining methods. The approach is tested for water and an aqueous glucose solution, and the results from the new implementation for coarse-grained molecular dynamics simulation show remarkable agreement with the dynamics obtained f...
متن کاملA coarse graining method for the identification of transition rates between molecular conformations.
The coarse graining method to be advocated in this paper consists of two main steps. First, the propagation of an ensemble of molecular states is described as a Markov chain by a transition probability matrix in a finite state space. Second, we obtain metastable conformations by an aggregation of variables via Robust Perron Cluster Analysis (PCCA+). Up to now, it has been an open question as to...
متن کاملEffective force coarse-graining.
An effective force coarse-graining (EF-CG) method is presented in this paper that complements the more general multiscale coarse-graining (MS-CG) methodology. The EF-CG method determines effective pairwise forces between coarse-grained sites by averaging over the atomistic forces between the corresponding atomic groups in configurations sampled from equilibrium all-atom molecular dynamics simul...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Physical chemistry chemical physics : PCCP
دوره 13 22 شماره
صفحات -
تاریخ انتشار 2011