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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Karplus, Martin Ovchinnikov, Victor Cecchini, Marco |
| Description | Author Affiliation: Ovchinnikov V ( Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA. ovchinnv@georgetown.edu) |
| Abstract | A simple and robust formulation of the path-independent confinement method for the calculation of free energies is presented. The simplified confinement method (SCM) does not require matrix diagonalization or switching off the molecular force field, and has a simple convergence criterion. The method can be readily implemented in molecular dynamics programs with minimal or no code modifications. Because the confinement method is a special case of thermodynamic integration, it is trivially parallel over the integration variable. The accuracy of the method is demonstrated using a model diatomic molecule, for which exact results can be computed analytically. The method is then applied to the alanine dipeptide in vacuum, and to the -helix â ß-sheet transition in a 16-residue peptide modeled in implicit solvent. The SCM requires less effort for the calculation of free energy differences than previous formulations because it does not require computing normal modes. The SCM has a diminished advantage for determining absolute free energy values, because it requires decreasing the MD integration step to obtain accurate results. An approximate confinement procedure is introduced, which can be used to estimate directly the configurational entropy difference between two macrostates, without the need for additional computation of the difference in the free energy or enthalpy. The approximation has convergence properties similar to those of the standard confinement method for the calculation of free energies. The use of the approximation requires about 5 times less wall-clock simulation time than that needed to compute enthalpy differences to similar precision from an MD trajectory. For the biomolecular systems considered in this study, the errors in the entropy approximation are under 10%. Practical applications of the methods to proteins are currently limited to implicit solvent simulations. |
| ISSN | 15206106 |
| e-ISSN | 15205207 |
| Journal | The Journal of Physical Chemistry B |
| Issue Number | 3 |
| Volume Number | 117 |
| Language | English |
| Publisher | American Chemical Society (United States) |
| Publisher Date | 2013-01-24 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Peptides Chemistry Solvents Bacterial Proteins Entropy Molecular Dynamics Simulation Protein Structure, Secondary Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't Physical chemistry |
| Content Type | Text |
| Resource Type | Article |
| Subject | Surfaces, Coatings and Films Materials Chemistry Medicine Physical and Theoretical Chemistry |
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