Accurate and efficient corrections for missing dispersion interactions in molecular simulations.
In simulations, molecular dispersion interactions are frequently neglected beyond a cutoff of around 1 nm. In some cases, analytical corrections appropriate for isotropic systems are applied to the pressure and/or the potential energy. Here, we show that in systems containing macromolecules, either of these approaches introduce statistically significant errors in some observed properties; for example, the choice of cutoff can affect computed free energies of ligand binding to proteins by 1 to 2 kcal/mol. We review current methods for eliminating this cutoff-dependent behavior of the dispersion energy and identify some situations where they fail. We introduce two new formalisms, appropriate for binding free energy calculations, which overcome these failings, requiring minimal computational effort beyond the time required to run the original simulation. When these cutoff approximations are applied, which can be done after all simulations are completed, results are consistent across simulations run with different cutoffs. In many situations, simulations can be run with even shorter cutoffs than typically used, resulting in increased computational efficiency.
Shirts
Michael R
MR
Department of Chemistry, Columbia University, New York, New York 10027, USA. michael.shirts@columbia.edu
Mobley
David L
DL
Chodera
John D
JD
Pande
Vijay S
VS
D003198:Computer Simulation; D008024:Ligands; D008956:Models, Chemical; D011485:Protein Binding; D012997:Solvents; D016559:Tacrolimus / Q000737:chemistry* / Q000378:metabolism; D022061:Tacrolimus Binding Protein 1A / Q000737:chemistry* / Q000378:metabolism; D013816:Thermodynamics
D008024:Ligands; D012997:Solvents; D022061:Tacrolimus Binding Protein 1A; D016559:Tacrolimus