2008
DOI: 10.1021/ct8003386
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Implementation of Umbrella Integration within the Framework of the Empirical Valence Bond Approach

Abstract: The umbrella integration method for calculating the potential of mean force (PMF) for a chemical reaction is implemented within the empirical valence bond (EVB) framework. In this implementation, the PMF is generated along the energy gap reaction coordinate, and the biasing potential is the difference between the mapping potential, which is defined to be a linear combination of the valence bond state energies, and the EVB ground state energy. The umbrella integration method is based on the derivative of the PM… Show more

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Cited by 16 publications
(25 citation statements)
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“…The RMSD distributions reveal that Zn 2 •CzrA exists in a single conformational state situated in a deep potential well with very steep walls; this ensures that a severe energetic penalty is incurred for moving away from the minima in this allosterically inhibited form. 58 In striking contrast, the population distribution for Apo•CzrA suggests at least three distinguishable conformational states defined by a shallow potential well with each state separated by a few kcal/mol from the minima. One of these states qualitatively resembles the Zn(II) bound allosteric state consistent with the idea that apo-CzrA is capable of making conformational excursions into a Zn(II) bound like structure.…”
Section: Resultsmentioning
confidence: 92%
“…The RMSD distributions reveal that Zn 2 •CzrA exists in a single conformational state situated in a deep potential well with very steep walls; this ensures that a severe energetic penalty is incurred for moving away from the minima in this allosterically inhibited form. 58 In striking contrast, the population distribution for Apo•CzrA suggests at least three distinguishable conformational states defined by a shallow potential well with each state separated by a few kcal/mol from the minima. One of these states qualitatively resembles the Zn(II) bound allosteric state consistent with the idea that apo-CzrA is capable of making conformational excursions into a Zn(II) bound like structure.…”
Section: Resultsmentioning
confidence: 92%
“…Next, the solvated protein was energy minimized and equilibrated using a well-defined procedure (Chakravorty et al 2009; Chakravorty et al 2008; Chakravorty and Hammes-Schiffer 2010). NOE restraints with a force constant of 30 kcal/mol•Å 2 were applied to the protein structure over the course of the equilibration process.…”
Section: Methods and Applicationmentioning
confidence: 99%
“…Well-established protocols were used to simulate the protein and protein-DNA complexes in our studies (Chakravorty & Hammes-Schiffer, 2010;Chakravorty, Kumarasiri, Soudackov, & Hammes-Schiffer, 2008;Chakravorty, Soudackov, & Hammes-Schiffer, 2009). All classical MD simulations were performed using the AMBER 11 suite of programs on a potential energy surface described by the AMBER ff99SB force field with parambsc0 modifications for DNA (Case et al, 2010).…”
Section: Simulation Protocolsmentioning
confidence: 99%