Activated processes can be studied in the molecular dynamics (MD) approach by imposing a mechanical constraint on the corresponding reaction coordinate and by performing a kind of thermodynamic integration. The blue-moon ensemble method provides us with the correct algorithm for computing the potential of mean force and the transmission coefficient. Here we show a procedure for;obtaining the mean force directly from the average force of constraint and a geometric correction term which is easy to compute in MD simulations. Previous work on the same problem will be also discussed. (C) 1998 American Institute of Physics
Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulat...
ABSTRACT: The calculations of potential of mean force along complex chemical reactions or rare event...
The aim of this mini-review article is to clarify the relation between two distinct formulations of ...
Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the...
In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium c...
Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the...
Abstract. Activated processes from chemical reactions up to confor-mational transitions of large bio...
We give a new formula expressing the components of the mean force in terms of a conditional expectat...
The potential of mean force (PMF) calculation in single molecule manipulation experiments performed ...
In this paper we set out to derive a relation between the constraint force and the derivative of the...
The potential of mean force (PMF) calculation in single molecule manipulation experiments performed ...
In classical molecular dynamics free energy is one of the most important quantities in analyzing a m...
One common objective of molecular simulations in chemistry and biology is to calcu-late the free ene...
101 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2004.This thesis explores the issu...
In the context of molecular dynamics simulations of rare events, the application of constraints on a...
Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulat...
ABSTRACT: The calculations of potential of mean force along complex chemical reactions or rare event...
The aim of this mini-review article is to clarify the relation between two distinct formulations of ...
Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the...
In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium c...
Recently Tobias and Broods introduced a method to compute by molecular dynamics with constraints the...
Abstract. Activated processes from chemical reactions up to confor-mational transitions of large bio...
We give a new formula expressing the components of the mean force in terms of a conditional expectat...
The potential of mean force (PMF) calculation in single molecule manipulation experiments performed ...
In this paper we set out to derive a relation between the constraint force and the derivative of the...
The potential of mean force (PMF) calculation in single molecule manipulation experiments performed ...
In classical molecular dynamics free energy is one of the most important quantities in analyzing a m...
One common objective of molecular simulations in chemistry and biology is to calcu-late the free ene...
101 p.Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2004.This thesis explores the issu...
In the context of molecular dynamics simulations of rare events, the application of constraints on a...
Constraints are convenient in the calculation of free energy profiles via molecular dynamics simulat...
ABSTRACT: The calculations of potential of mean force along complex chemical reactions or rare event...
The aim of this mini-review article is to clarify the relation between two distinct formulations of ...