596 research outputs found
Building Water Models, A Different Approach
Simplified, classical models of water are an integral part of atomistic
molecular simulations, especially in biology and chemistry where hydration
effects are critical. Yet, despite several decades of effort, these models are
still far from perfect. Presented here is an alternative approach to
constructing point charge water models - currently, the most commonly used
type. In contrast to the conventional approach, we do not impose any geometry
constraints on the model other than symmetry. Instead, we optimize the
distribution of point charges to best describe the "electrostatics" of the
water molecule, which is key to many unusual properties of liquid water. The
search for the optimal charge distribution is performed in 2D parameter space
of key lowest multipole moments of the model, to find best fit to a small set
of bulk water properties at room temperature. A virtually exhaustive search is
enabled via analytical equations that relate the charge distribution to the
multipole moments. The resulting "optimal" 3-charge, 4-point rigid water model
(OPC) reproduces a comprehensive set of bulk water properties significantly
more accurately than commonly used rigid models: average error relative to
experiment is 0.76%. Close agreement with experiment holds over a wide range of
temperatures, well outside the ambient conditions at which the fit to
experiment was performed. The improvements in the proposed water model extend
beyond bulk properties: compared to the common rigid models, predicted
hydration free energies of small molecules in OPC water are uniformly closer to
experiment, root-mean-square error < 1kcal/mol
Development of an Advanced Force Field for Water using Variational Energy Decomposition Analysis
Given the piecewise approach to modeling intermolecular interactions for
force fields, they can be difficult to parameterize since they are fit to data
like total energies that only indirectly connect to their separable functional
forms. Furthermore, by neglecting certain types of molecular interactions such
as charge penetration and charge transfer, most classical force fields must
rely on, but do not always demonstrate, how cancellation of errors occurs among
the remaining molecular interactions accounted for such as exchange repulsion,
electrostatics, and polarization. In this work we present the first generation
of the (many-body) MB-UCB force field that explicitly accounts for the
decomposed molecular interactions commensurate with a variational energy
decomposition analysis, including charge transfer, with force field design
choices that reduce the computational expense of the MB-UCB potential while
remaining accurate. We optimize parameters using only single water molecule and
water cluster data up through pentamers, with no fitting to condensed phase
data, and we demonstrate that high accuracy is maintained when the force field
is subsequently validated against conformational energies of larger water
cluster data sets, radial distribution functions of the liquid phase, and the
temperature dependence of thermodynamic and transport water properties. We
conclude that MB-UCB is comparable in performance to MB-Pol, but is less
expensive and more transferable by eliminating the need to represent
short-ranged interactions through large parameter fits to high order
polynomials
Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning
Classical intermolecular potentials typically require an extensive
parametrization procedure for any new compound considered. To do away with
prior parametrization, we propose a combination of physics-based potentials
with machine learning (ML), coined IPML, which is transferable across small
neutral organic and biologically-relevant molecules. ML models provide
on-the-fly predictions for environment-dependent local atomic properties:
electrostatic multipole coefficients (significant error reduction compared to
previously reported), the population and decay rate of valence atomic
densities, and polarizabilities across conformations and chemical compositions
of H, C, N, and O atoms. These parameters enable accurate calculations of
intermolecular contributions---electrostatics, charge penetration, repulsion,
induction/polarization, and many-body dispersion. Unlike other potentials, this
model is transferable in its ability to handle new molecules and conformations
without explicit prior parametrization: All local atomic properties are
predicted from ML, leaving only eight global parameters---optimized once and
for all across compounds. We validate IPML on various gas-phase dimers at and
away from equilibrium separation, where we obtain mean absolute errors between
0.4 and 0.7 kcal/mol for several chemically and conformationally diverse
datasets representative of non-covalent interactions in biologically-relevant
molecules. We further focus on hydrogen-bonded complexes---essential but
challenging due to their directional nature---where datasets of DNA base pairs
and amino acids yield an extremely encouraging 1.4 kcal/mol error. Finally, and
as a first look, we consider IPML in denser systems: water clusters,
supramolecular host-guest complexes, and the benzene crystal.Comment: 15 pages, 9 figure
Improvements to the APBS biomolecular solvation software suite
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
understanding solvation and electrostatics in biomedical applications: accurate
and efficient models for biomolecular solvation and electrostatics, robust and
scalable software for applying those theories to biomolecular systems, and
mechanisms for sharing and analyzing biomolecular electrostatics data in the
scientific community. To address new research applications and advancing
computational capabilities, we have continually updated APBS and its suite of
accompanying software since its release in 2001. In this manuscript, we discuss
the models and capabilities that have recently been implemented within the APBS
software package including: a Poisson-Boltzmann analytical and a
semi-analytical solver, an optimized boundary element solver, a geometry-based
geometric flow solvation model, a graph theory based algorithm for determining
p values, and an improved web-based visualization tool for viewing
electrostatics
- …