Big Chemical Encyclopedia

Chemical substances, components, reactions, process design ...

Articles Figures Tables About

Free-energy simulations

When equation 7.20 is differentiated, the following result is obtained  [Pg.247]

Recalling the form of the Helmholtz free energy, A = U — TS, the following derivations are easily carried out  [Pg.247]

Therefore, simulations can be performed in which the force field is gradually turned on over the system, accumulating work from the computational work supplier, and use the fundamental relationship w AA to obtain an upper boundary for the free energy variation. This way of proceeding [23] is obviously rather complicated and computationally demanding. [Pg.248]

Alternative procedures must be found. Given the expression 7.41 for the statistical entropy, one obtains, after some algebra  [Pg.248]

Consider a state a described by a hamiltonian // = ( pot + kin)a. evolving toward a second state P and a parameter X such that for any value of this parameter the hamiltonian is given by [Pg.248]


Boresch, S., Archontis, G., Karplus, M. Free energy simulations The meaning of the individual contributions from component analysis. Proteins Str. Funct. Genet., 20 (1994) 25-33... [Pg.146]

Hermans, J. A simple analysis of noise and hysteresis in free energy simulations. J. Phys. Chem. 95 (1991) 9029-9032... [Pg.146]

Conformational free energy simulations are being widely used in modeling of complex molecular systems [1]. Recent examples of applications include study of torsions in n-butane [2] and peptide sidechains [3, 4], as well as aggregation of methane [5] and a helix bundle protein in water [6]. Calculating free energy differences between molecular states is valuable because they are observable thermodynamic quantities, related to equilibrium constants and... [Pg.163]

Table 3. Conformational free energy simulation of linear DPDPE. Changes in free energy and its components. Units kcal/mol... Table 3. Conformational free energy simulation of linear DPDPE. Changes in free energy and its components. Units kcal/mol...
K. Kuczera. One- and multidimensional conformational free energy simulations. J. Comp. Chem., 17 1726-1749, 1996. [Pg.174]

Mezei M and D L Beveridge 1986. Free Energy Simulations. In Beveridge D L and W L Jorgens (Editors) Computer Simulation of Chemical and Biomolecular Systems. Annals of the New Y Academy of Sciences 482 1-23. [Pg.649]

Boresch S, G Archontis and M Karplus 1994. Free Energy Simulations The Meaning of the Indi-. id Contributions from a Component. Analysis. Proteins Structure, Function and Gau tics 20 25-33. [Pg.649]

Sir Isaac Newton spent much of his life pursuing an elusive dream, the transmutation of base materials into gold. Though he was not successful during his lifetime, he did manage to discover the equations of motion that, tliree centuries later, make alchemy possible on a computer. To perfonn this feat, Newton s equations need only be supplemented by the modem technology of free energy simulations. [Pg.169]

Another variant that may mrn out to be the method of choice performs the alchemical free energy simulation with a spherical model surrounded by continuum solvent, neglecting portions of the macromolecule that lie outside the spherical region. The reaction field due to the outer continuum is easily included, because the model is spherical. Additional steps are used to change the dielectric constant of that portion of the macromolecule that lies in the outer region from its usual low value to the bulk solvent value (before the alchemical simulation) and back to its usual low value (after the alchemical simulation) the free energy for these steps can be obtained from continuum electrostatics [58]. [Pg.189]

Finally, an alchemical free energy simulation is needed to obtain the free energy difference between any one substate of system A and any one substate of system B, e.g., Ai- In practice, one chooses two substates that resemble each other as much as possible. In the alchemical simulation, it is necessary to restrain appropriate parts of the system to remain in the chosen substate. Thus, for the present hybrid Asp/Asn molecule, the Asp side chain should be confined to the Asp substate I and the Asn side chain confined to its substate I. Flat-bottomed dihedral restraints can achieve this very conveniently [38], in such a way that the most populated configurations (near the energy minimum) are hardly perturbed by the restraints. Note that if the substates AI and BI differ substantially, the transfomnation will be difficult to perform with a single-topology approach. [Pg.193]

A powerful and general technique to enhance sampling is the use of umbrella potentials, discussed in Section IV. In the context of alchemical free energy simulations, for example, umbrella potentials have been used both to bias the system toward an experimentally determined conformation [26] and to promote conformational transitions by reducing dihedral and van der Waals energy terms involving atoms near a mutation site [67]. [Pg.194]

A Tropsha, J Hermans. Application of free energy simulations to the binding of a transition-state-analogue inhibitor to HIV protease. Protein Eng 51 29-34, 1992. [Pg.366]

Free energy simulations are a useful means of quantitating whether the free energy and not simply the energy is shifting in the predicted manner for the mutant (see Chapter 9). The difference in the free energy changes upon reduction between a wild-type and a mutant, AAG = AG — AG, where the asterisk indicates the mutant, can be calculated in two ways via the thennodynamic cycle shown in Scheme 2,... [Pg.407]

Bitetti-Putzer, R. Yang, W. Karplus, M., Generalized ensembles serve to improve the convergence of free energy simulations, Chem. Phys. Lett. 2003, 377, 633-641... [Pg.29]

Simonson, T. Archontis, G. Karplus, M., Free energy simulations come of age protein-ligand recognition, Acc. Chem. Res. 2002, 35, 430-437... [Pg.32]

Rodinger, T. Pomes, R., Enhancing the accuracy, the efficiency and the scope of free energy simulations, Curr. Opin. Struct. Biol. 2005,15,164-170... [Pg.32]


See other pages where Free-energy simulations is mentioned: [Pg.163]    [Pg.164]    [Pg.169]    [Pg.170]    [Pg.172]    [Pg.174]    [Pg.499]    [Pg.85]    [Pg.140]    [Pg.171]    [Pg.181]    [Pg.191]    [Pg.194]    [Pg.195]    [Pg.353]    [Pg.362]    [Pg.363]    [Pg.365]    [Pg.400]    [Pg.401]    [Pg.403]    [Pg.80]    [Pg.181]    [Pg.181]    [Pg.182]    [Pg.193]    [Pg.267]    [Pg.268]    [Pg.391]    [Pg.393]    [Pg.433]   
See also in sourсe #XX -- [ Pg.362 , Pg.403 , Pg.407 ]

See also in sourсe #XX -- [ Pg.69 ]

See also in sourсe #XX -- [ Pg.2 ]




SEARCH



Alchemical free energy simulations

Approximate free energy simulations

Computer simulation free energy calculation difficulties

Energy simulation

Free Energies from Transition Path Sampling Simulations

Free Energy and the Entropy of Macromolecular Systems by Computer Simulation

Free Energy by Molecular Simulation

Free energy calculations simulation methods

Free energy from simulations

Free energy methods simulation techniques

Free energy perturbation Monte Carlo simulations

Free energy perturbation simulations

Free energy simulations error analysis

Free energy simulations, types

Free energy simulations, types Monte Carlo

Free energy simulations, types molecular dynamics

Free-energy simulations, hydration

Helmholtz free energy computer simulation

Molecular dynamics simulation free energy calculations

Molecular dynamics simulation free energy perturbation

Molecular dynamics simulations electrostatic free energies

Molecular simulations free energy perturbations

Monte Carlo simulation free energy calculations

Monte Carlo simulations free-energy

Rigorous free energy simulations

Simulations free energy profiles

Theoretical Simulations of Free Energy Relationships in Proton Transfer

© 2024 chempedia.info