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Subsections


Solute Scaling and REST2

Solute scaling improves sampling efficiency by scaling the intramolecular potential energy of a protein to lower barriers separating different confirmations [79]. The potential is scaled based on a parameter $ \beta$ ,

$\displaystyle U^{\text{SS}}(\vec{r}) = \beta U_{\text{pp}}(\vec{r}) + \sqrt{\beta} U_{\text{pw}}(\vec{r}) + U_{\text{ww}}(\vec{r}),$ (49)

with $ U_{\text{pp}}$ denoting protein-protein interactions, $ U_{\text{pw}}$ denoting protein-water interactions, and $ U_{\text{ww}}$ denoting water-water interactions, effectively ``heating'' the protein's interatomic interactions whenever $ \beta < 1$ . The NAMD implementation is made efficient by rescaling the force field parameters for the affected atoms [31]. In particular, this parameter scaling approach makes the calculation compatible with existing CUDA force kernels.

The NAMD implementation provides additional flexibility to solute scaling by allowing different scaling factors for electrostatics, van der Waals, and bonded interactions, as described in the following section. Solute scaling can be combined with replica exchange to produce a powerful sampling enhancement method that is highly transferable and provides higher efficiency than traditional temperature exchange methods. In the literature, this replica exchange solute scaling method is known as REST2, due to its improvement of the earlier REST (replica exchange solute tempering) method that directly scaled the temperature of the solute. Sample files are available in directory lib/replica/REST2, with script file lib/replica/REST2/rest2_remd.namd demonstrating use of solute scaling with multiple replicas.

NAMD parameters

The following parameters are used to control solute scaling:


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