16 research outputs found
Bayesian selection for coarse-grained models of liquid water
The necessity for accurate and computationally efficient representations of
water in atomistic simulations that can span biologically relevant timescales
has born the necessity of coarse-grained (CG) modeling. Despite numerous
advances, CG water models rely mostly on a-priori specified assumptions. How
these assumptions affect the model accuracy, efficiency, and in particular
transferability, has not been systematically investigated. Here we propose a
data driven, comparison and selection for CG water models through a
Hierarchical Bayesian framework. We examine CG water models that differ in
their level of coarse-graining, structure, and number of interaction sites. We
find that the importance of electrostatic interactions for the physical system
under consideration is a dominant criterion for the model selection. Multi-site
models are favored, unless the effects of water in electrostatic screening are
not relevant, in which case the single site model is preferred due to its
computational savings. The charge distribution is found to play an important
role in the multi-site model's accuracy while the flexibility of the
bonds/angles may only slightly improve the models. Furthermore, we find
significant variations in the computational cost of these models. We present a
data informed rationale for the selection of CG water models and provide
guidance for future water model designs
Learning neural network potentials from experimental data via Differentiable Trajectory Reweighting
In molecular dynamics (MD), neural network (NN) potentials trained bottom-up
on quantum mechanical data have seen tremendous success recently. Top-down
approaches that learn NN potentials directly from experimental data have
received less attention, typically facing numerical and computational
challenges when backpropagating through MD simulations. We present the
Differentiable Trajectory Reweighting (DiffTRe) method, which bypasses
differentiation through the MD simulation for time-independent observables.
Leveraging thermodynamic perturbation theory, we avoid exploding gradients and
achieve around 2 orders of magnitude speed-up in gradient computation for
top-down learning. We show effectiveness of DiffTRe in learning NN potentials
for an atomistic model of diamond and a coarse-grained model of water based on
diverse experimental observables including thermodynamic, structural and
mechanical properties. Importantly, DiffTRe also generalizes bottom-up
structural coarse-graining methods such as iterative Boltzmann inversion to
arbitrary potentials. The presented method constitutes an important milestone
towards enriching NN potentials with experimental data, particularly when
accurate bottom-up data is unavailable.Comment: This is a post-peer-review, pre-copyedit version of an article
published in Nature Communications. The final authenticated version is
available online at: http://dx.doi.org/10.1038/s41467-021-27241-
Accurate machine learning force fields via experimental and simulation data fusion
Machine Learning (ML)-based force fields are attracting ever-increasing
interest due to their capacity to span spatiotemporal scales of classical
interatomic potentials at quantum-level accuracy. They can be trained based on
high-fidelity simulations or experiments, the former being the common case.
However, both approaches are impaired by scarce and erroneous data resulting in
models that either do not agree with well-known experimental observations or
are under-constrained and only reproduce some properties. Here we leverage both
Density Functional Theory (DFT) calculations and experimentally measured
mechanical properties and lattice parameters to train an ML potential of
titanium. We demonstrate that the fused data learning strategy can concurrently
satisfy all target objectives, thus resulting in a molecular model of higher
accuracy compared to the models trained with a single data source. The
inaccuracies of DFT functionals at target experimental properties were
corrected, while the investigated off-target properties remained largely
unperturbed. Our approach is applicable to any material and can serve as a
general strategy to obtain highly accurate ML potentials
Order and interactions in DNA arrays: Multiscale molecular dynamics simulation
While densely packed DNA arrays are known to exhibit hexagonal and orthorhombic local packings, the detailed mechanism governing the associated phase transition remains rather elusive. Furthermore, at high densities the atomistic resolution is paramount to properly account for fine details, encompassing the DNA molecular order, the contingent ordering of counterions and the induced molecular ordering of the bathing solvent, bringing together electrostatic, steric, thermal and direct hydrogen-bonding interactions, resulting in the observed osmotic equation of state. We perform a multiscale simulation of dense DNA arrays by enclosing a set of 16 atomistically resolved DNA molecules within a semi-permeable membrane, allowing the passage of water and salt ions, and thus mimicking the behavior of DNA arrays subjected to external osmotic stress in a bathing solution of monovalent salt and multivalent counterions. By varying the DNA density, local packing symmetry, and counterion type, we obtain osmotic equation of state together with the hexagonal-orthorhombic phase transition, and full structural characterization of the DNA subphase in terms of its positional and angular orientational fluctuations, counterion distributions, and the solvent local dielectric response profile with its order parameters that allow us to identify the hydration force as the primary interaction mechanism at high DNA densities.ISSN:2045-232
SWINGER:A clustering algorithm for concurrent coupling of atomistic and supramolecular liquids
In this contribution, we review recent developments and applications of a dynamic clustering algorithm SWINGER tailored for the multiscale molecular simulations of biomolecular systems. The algorithm on-the-fly redistributes solvent molecules among supramolecular clusters. In particular, we focus on its applications in combination with the adaptive resolution scheme, which concurrently couples atomistic and coarse-grained molecular representations. We showcase the versatility of our multiscale approach on a few applications to biomolecular systems coupling atomistic and supramolecular water models such as the well-established MARTINI and dissipative particle dynamics models and provide an outlook for future work
Adaptive resolution simulation of polarizable supramolecular coarse-grained water models
Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties. (C) 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License
Bayesian selection for coarse-grained models of liquid water
The necessity for accurate and computationally efficient representations of water in atomistic simulations that can span biologically relevant timescales has born the necessity of coarse-grained (CG) modeling. Despite numerous advances, CG water models rely mostly on a-priori specified assumptions. How these assumptions affect the model accuracy, efficiency, and in particular transferability, has not been systematically investigated. Here we propose a data driven comparison and selection for CG water models through a Hierarchical Bayesian framework. We examine CG water models that differ in their level of coarse-graining, structure, and number of interaction sites. We find that the importance of electrostatic interactions for the physical system under consideration is a dominant criterion for the model selection. Multi-site models are favored, unless the effects of water in electrostatic screening are not relevant, in which case the single site model is preferred due to its computational savings. The charge distribution is found to play an important role in the multi-site model’s accuracy while the flexibility of the bonds/angles may only slightly improve the models. Furthermore, we find significant variations in the computational cost of these models. We present a data informed rationale for the selection of CG water models and provide guidance for future water model designs.ISSN:2045-232
Molecular dynamics simulation of high density DNA arrays
Densely packed DNA arrays exhibit hexagonal and orthorhombic local packings, as well as a weakly first order transition between them. While we have some understanding of the interactions between DNA molecules in aqueous ionic solutions, the structural details of its ordered phases and the mechanism governing the respective phase transitions between them remains less well understood. Since at high DNA densities, i.e., small interaxial spacings, one can neither neglect the atomic details of the interacting macromolecular surfaces nor the atomic details of the intervening ionic solution, the atomistic resolution is a sine qua non to properly describe and analyze the interactions between DNA molecules. In fact, in order to properly understand the details of the observed osmotic equation of state, one needs to implement multiple levels of organization, spanning the range from the molecular order of DNA itself, the possible ordering of counterions, and then all the way to the induced molecular ordering of the aqueous solvent, all coupled together by electrostatic, steric, thermal and direct hydrogen-bonding interactions. Multiscale simulations therefore appear as singularly suited to connect the microscopic details of this system with its macroscopic thermodynamic behavior. We review the details of the simulation of dense atomistically resolved DNA arrays with different packing symmetries and the ensuing osmotic equation of state obtained by enclosing a DNA array in a monovalent salt and multivalent (spermidine) counterions within a solvent permeable membrane, mimicking the behavior of DNA arrays subjected to external osmotic stress. By varying the DNA density, the local packing symmetry, and the counterion type, we are able to analyze the osmotic equation of state together with the full structural characterization of the DNA subphase, the counterion distribution and the solvent structural order in terms of its different order parameters and consequently identify the most important contribution to the DNA-DNA interactions at high DNA densities