Paper Citing NAMD - Abstract
Orsi, Mario; Ding, Wei; Palaiokostas, Michail
Direct Mixing of Atomistic Solutes and Coarse-Grained Water
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10:4684-4693, OCT 2014
We present a new dual-resolution approach for coupling atomistic and coarse-grained models in molecular dynamics simulations of hydrated systems. In particular, a coarse-grained point dipolar water model is used to solvate molecules represented with standard all-atom force fields. A unique characteristic of our methodology is that the mixing of resolutions is direct, meaning that no additional or ad hoc scaling factors, intermediate regions, or extra sites are required. To validate the methodology, we compute the hydration free energy of 14 atomistic small molecules (analogs of amino acid side chains) solvated by the coarse-grained water. Remarkably, our predictions reproduce the experimental data as accurately as the predictions from state-of-the-art fully atomistic simulations. We also show that the hydration free energy of the coarse-grained water itself is in comparable or better agreement with the experimental value than the predictions from all but one of the most common multisite atomistic models. The coarse-grained water is then applied to solvate a typical atomistic protein containing both alpha-helix and beta-strand elements. Moreover, parallel tempering simulations are performed to investigate the folding free energy landscape of a representative alpha helical and a beta hairpin structure. For the simulations considered in this work, our dual-resolution method is found to be 3 to 6 times more computationally efficient than corresponding fully atomistic approaches.
