Incorporating the effect of ionic strength in free energy calculations using explicit ions
2004 Wiley Periodicals, Inc.
| Veröffentlicht in: | Journal of computational chemistry. - 1984. - 26(2005), 2 vom: 30. Jan., Seite 115-22 |
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| 1. Verfasser: | |
| Weitere Verfasser: | , , |
| Format: | Aufsatz |
| Sprache: | English |
| Veröffentlicht: |
2005
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| Zugriff auf das übergeordnete Werk: | Journal of computational chemistry |
| Schlagworte: | Journal Article Enzyme Inhibitors Triose-Phosphate Isomerase EC 5.3.1.1 |
| Zusammenfassung: | 2004 Wiley Periodicals, Inc. The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors calculated at five different ion concentrations is used as an example. We show that the free energy difference can be highly sensitive to the presence of explicit ions even in cases where the mutation itself does not involve a change in the overall charge. The effect is most significant if the molecule carries a net charge close to the site mutated. Furthermore, it is shown that the introduction of a small number of ions can lead to very severe sampling problems suggesting that in practical calculations convergence can best be achieved by incorporating either no counterions or by simulating at high ionic strength to ensure sufficient sampling of the ion distribution |
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| Beschreibung: | Date Completed 02.02.2005 Date Revised 15.12.2004 published: Print Citation Status MEDLINE |
| ISSN: | 1096-987X |