Related papers: Continual Model of Medium IV: Calculation of analy…
The problem of finding of analytical gradients (derivatives over atoms coordinates) of solvation energies can be decomposed on two subtasks: at the first stage we search for parameters of the superficial devices (three coordinates, three…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
Several implicit (continuum) solvent models are considered: the Polarized Continuum Model (PCM), the Surface Generalized Born model (SGB), and the COnductor-like Screening model (COSMO) as well as their implementation in the form of the…
In the given paper the algorithm describing original and universal principles of a triangulation of a smooth molecular surface: solvent excluding solvent (SES), received by primary and secondary rolling, and solvent accessible surface (SAS)…
Classically, surface tension is seen as a force per unit length or as energy per unit area. The surface energy is calculated thermodynamically on the surface of a mathematical layer with no thickness. The surface energy concept is certainly…
The analytic energy gradients in the atomic orbital representation have recently been published (J. Chem. Phys. 146, 014102, 2017) within the framework of the natural orbital functional theory (NOFT). We provide here an alternative…
The role of numerical accuracy in training and evaluating neural network-based potential energy surfaces is examined for different experimental observables. For observables that require third- and fourth-order derivatives of the total…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
The theoretical investigation of gas adsorption, storage, separation, diffusion and related transport processes in porous materials relies on a detailed knowledge of the potential energy surface of molecules in a stationary environment. In…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
Earlier, normalization conditions for the columns of the PCM (Polarized Continuum Model) were determined and a method of enlarged surface meshes was developed. We developed similar methods for the COSMO (COnductor like Screening MOdel).…
We report a development of a new fast surface-based method for numerical calculations of solvation energy of biomolecules with a large number of charged groups. The procedure scales linearly with the system size both in time and memory…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
We develop an alternative formulation in the energy-domain to calculate the second order M{\o}ller-Plesset (MP2) perturbation energies. The approach is based on repeatedly choosing four random energies using a non-separable guiding…
It is shown that the quadrature derivatives in some analytical gradients of energies evaluated with a multi-centre radial-angular grid do not vanish even in the limit of an infinitely dense grid, causing severe errors when neglected. The…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
This paper develops methodology for local sensitivity analysis based on directional derivatives associated with spatial processes. Formal gradient analysis for spatial processes was elaborated in previous papers, focusing on distribution…
We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of…
Analytic energy gradients with respect to nuclear motion are derived for non-singlet compounds in the natural orbital functional theory. We exploit the formulation for multiplets in order to obtain a simple formula valid for any…
An iterative method for calculating the polar component of the solvation Gibbs energy under a smooth change in dielectric permittivity, both between a substrate and a solvent and in a solvent is formulated on the basis of a previously…