On the use of orientational restraints and symmetry corrections in alchemical free energy calculations.

@article{Mobley2006OnTU,
  title={On the use of orientational restraints and symmetry corrections in alchemical free energy calculations.},
  author={David L. Mobley and John D. Chodera and Ken A. Dill},
  journal={The Journal of chemical physics},
  year={2006},
  volume={125 8},
  pages={084902}
}
Alchemical free energy calculations are becoming a useful tool for calculating absolute binding free energies of small molecule ligands to proteins. Here, we find that the presence of multiple metastable ligand orientations can cause convergence problems when distance restraints alone are used. We demonstrate that the use of orientational restraints can greatly accelerate the convergence of these calculations. However, even with this acceleration, we find that sufficient sampling requires… CONTINUE READING

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