Name
Title | ||
|---|---|---|
Predicting hydration free energies using all-atom molecular dynamics simulations and multiple starting conformations. |
Abstract | ||
|---|---|---|
Molecular dynamics simulations in explicit solvent were applied to predict the hydration free energies for 23 small organic
molecules in blind SAMPL2 test. We found good agreement with experimental results, with an RMS error of 2.82 kcal/mol over
the whole set and 1.86 kcal/mol over all the molecules except several hydroxyl-rich compounds where we find evidence for a
systematic error in the force field. We tested two different solvent models, TIP3P and TIP4P-Ew, and obtained very similar
hydration free energies for these two models; the RMS difference was 0.64 kcal/mol. We found that preferred conformation of
the carboxylic acids in water differs from that in vacuum. Surprisingly, this conformational change is not adequately sampled
on simulation timescales, so we apply an umbrella sampling technique to include free energies associated with the conformational
change. Overall, the results of this test reveal that the force field parameters for some groups of molecules (such as hydroxyl-rich
compounds) still need to be improved, but for most compounds, accuracy was consistent with that seen in our previous tests. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1007/s10822-010-9343-7 | Journal of computer-aided molecular design |
Keywords | DocType | Volume |
Hydration,Alchemical,Free energy,Molecular dynamics | Journal | 24 |
Issue | ISSN | Citations |
4 | 1573-4951 | 21 |
PageRank | References | Authors |
1.61 | 8 | 2 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Pavel V. Klimovich | 1 | 38 | 3.36 |
| David L. Mobley | 2 | 219 | 20.01 |