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106,559
Nonequilibrium measurements of free energy differences for microscopically reversible markovian systems
, 1998
"... An equality has recently been shown relating the free energy difference between two equilibrium ensembles of a system and an ensemble average of the work required to switch between these two configurations. In the present paper it is shown that this result can be derived under the assumption that th ..."
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Cited by 67 (1 self)
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An equality has recently been shown relating the free energy difference between two equilibrium ensembles of a system and an ensemble average of the work required to switch between these two configurations. In the present paper it is shown that this result can be derived under the assumption
Computer simulation results for the freeenergy difference between BDNA
, 2000
"... Abstract. The aim of the present work is to characterize by computer simulation the freeenergy difference between B and ZDNA in saline solutions. We use a new scheme to rigorously calculate the electrostatic contribution and we use it to test the theoretical predictions for a socalled ‘empty’ DN ..."
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Cited by 1 (0 self)
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Abstract. The aim of the present work is to characterize by computer simulation the freeenergy difference between B and ZDNA in saline solutions. We use a new scheme to rigorously calculate the electrostatic contribution and we use it to test the theoretical predictions for a socalled ‘empty
The Free Energy Differences Between 3Point Water Models
, 1998
"... This paper describes precise calculations to determine the free energy differences between 3point models of liquid water, using the method of thermodynamic integration and molecular dynamics. For the three models considered in this study the order of thermodynamic stability at 300 K and 1 atm press ..."
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This paper describes precise calculations to determine the free energy differences between 3point models of liquid water, using the method of thermodynamic integration and molecular dynamics. For the three models considered in this study the order of thermodynamic stability at 300 K and 1 atm
Systematic FiniteSampling Inaccuracy in Free Energy Differences and Other Nonlinear Quantities
, 2003
"... Systematic inaccuracy is inherent in any computational estimate of a nonlinear average, such as the free energy difference ∆F between two states or systems, because of the availability of only a finite number of data values, N. In previous work, we outlined the fundamental statistical description of ..."
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Cited by 2 (0 self)
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Systematic inaccuracy is inherent in any computational estimate of a nonlinear average, such as the free energy difference ∆F between two states or systems, because of the availability of only a finite number of data values, N. In previous work, we outlined the fundamental statistical description
A “fast growth ” method of computing free energy differences
, 2001
"... Let ∆F be the free energy difference between two equilibrium states of a system. An established method of numerically computing ∆F involves a single, long “switching simulation”, during which the system is driven reversibly from one state to the other (slow growth, or adiabatic switching). Here we s ..."
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Cited by 1 (0 self)
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Let ∆F be the free energy difference between two equilibrium states of a system. An established method of numerically computing ∆F involves a single, long “switching simulation”, during which the system is driven reversibly from one state to the other (slow growth, or adiabatic switching). Here we
Systematic Computational Inaccuracy in Free Energy Differences and Other Nonlinear Quantities
, 2002
"... Systematic inaccuracy is inherent in any computational estimate of a nonlinear average, such as the free energy difference ∆F between two states or systems, because of the availability of only a finite number of data values, N. In previous work, we outlined the fundamental statistical description of ..."
Abstract
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Systematic inaccuracy is inherent in any computational estimate of a nonlinear average, such as the free energy difference ∆F between two states or systems, because of the availability of only a finite number of data values, N. In previous work, we outlined the fundamental statistical description
Constructing Free Energy Approximations and Generalized Belief Propagation Algorithms
 IEEE Transactions on Information Theory
, 2005
"... Important inference problems in statistical physics, computer vision, errorcorrecting coding theory, and artificial intelligence can all be reformulated as the computation of marginal probabilities on factor graphs. The belief propagation (BP) algorithm is an efficient way to solve these problems t ..."
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Cited by 585 (13 self)
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the Bethe approximation, and corresponding generalized belief propagation (GBP) algorithms. We emphasize the conditions a free energy approximation must satisfy in order to be a “valid ” or “maxentnormal ” approximation. We describe the relationship between four different methods that can be used
Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems
 2004 J. Comput. Chem
"... Abstract: A promising method for calculating free energy differences F is to generate nonequilibrium data via “fastgrowth ” simulations or by experiments—and then use Jarzynski’s equality. However, a difficulty with using Jarzynski’s equality is that F estimates converge very slowly and unreliably ..."
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Cited by 3 (0 self)
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Abstract: A promising method for calculating free energy differences F is to generate nonequilibrium data via “fastgrowth ” simulations or by experiments—and then use Jarzynski’s equality. However, a difficulty with using Jarzynski’s equality is that F estimates converge very slowly and unreliably
Results 1  10
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106,559