Publishes on Spectroscopy and Quantum Chemical Studies, Protein Structure and Dynamics, Genomics and Chromatin Dynamics. 14 papers and 33.4k citations.
In molecular dynamics (MD) simulations the need often arises to maintain such parameters as temperature or pressure rather than energy and volume, or to impose gradients for studying transport properties in nonequilibrium MD. A method is described to realize coupling to an external bath with constant temperature or pressure with adjustable time constants for the coupling. The method is easily extendable to other variables and to gradients, and can be applied also to polyatomic molecules involving internal constraints. The influence of coupling time constants on dynamical variables is evaluated. A leap-frog algorithm is presented for the general case involving constraints with coupling to both a constant temperature and a constant pressure bath.
Abstract A simple point‐charge potential, developed earlier for the calculation of intermolecular forces in molecular‐dynamics simulations of liquid water, has been extended to include interactions between water molecules and polar groups of proteins. A complete potential for use in the simulation of protein dynamics in water is reported.
The potential utility and limitations of two methods to determine free energy differences from molecular dynamics simulations (MD) are studied. The computation of the free energy of hydration of the inert gases serves as a simple but illustrative example. Good results are obtained for the inert gases from a perturbation treatment, using a reference ensemble obtained from a MD simulation of a cavity in water, if these atoms are comparable in size to the cavity and the calculated free energy differences are small. This limits the applicability of the perturbation treatment of a small number of cases. Larger free energy differences can be obtained with reasonable accuracy from MD simulations with continuously changing interaction parameters. This integration method is more generally applicable, but makes an additional simulation necessary.
Thermodynamic quantities related to the solvation of hydrophobic solutes in water can be approximated by the application of scaled-particle theory. The crucial quantity is the Gibbs free energy of cavity formation. A series of six molecular-dynamics simulations of water including repulsive cavities of various sizes has been carried out. Using perturbation statistical mechanics, the free energy has been derived as a function of cavity radius up to 0.32 nm (0.32 nm approach of water oxygens to the cavity centre). The free energy agrees well with predictions from scaled-particle theory and the experimental surface tension is predicted to within 5%. The radial distribution of water molecules with respect to the cavity has been determined for five cavity sizes; for one size (radius of approach of water oxygens of 0.3 nm) the orientational distribution and the residence-time distribution in the hydration shells has been determined.