41 research outputs found
Momentum distribution, vibrational dynamics and the potential of mean force in ice
By analyzing the momentum distribution obtained from path integral and phonon
calculations we find that the protons in hexagonal ice experience an
anisotropic quasi-harmonic effective potential with three distinct principal
frequencies that reflect molecular orientation. Due to the importance of
anisotropy, anharmonic features of the environment cannot be extracted from
existing experimental distributions that involve the spherical average. The
full directional distribution is required, and we give a theoretical prediction
for this quantity that could be verified in future experiments. Within the
quasi-harmonic context, anharmonicity in the ground state dynamics of the
proton is substantial and has quantal origin, a finding that impacts the
interpretation of several spectroscopies
Blind protein structure prediction using accelerated free-energy simulations.
We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition
Displaced path integral formulation for the momentum distribution of quantum particles
The proton momentum distribution, accessible by deep inelastic neutron
scattering, is a very sensitive probe of the potential of mean force
experienced by the protons in hydrogen-bonded systems. In this work we
introduce a novel estimator for the end to end distribution of the Feynman
paths, i.e. the Fourier transform of the momentum distribution. In this
formulation, free particle and environmental contributions factorize. Moreover,
the environmental contribution has a natural analogy to a free energy surface
in statistical mechanics, facilitating the interpretation of experiments. The
new formulation is not only conceptually but also computationally advantageous.
We illustrate the method with applications to an empirical water model,
ab-initio ice, and one dimensional model systems
Nuclear quantum effects in water
In this work, a path integral Car-Parrinello molecular dynamics simulation of
liquid water is performed. It is found that the inclusion of nuclear quantum
effects systematically improves the agreement of first principles simulations
of liquid water with experiment. In addition, the proton momentum distribution
is computed utilizing a recently developed open path integral molecular
dynamics methodology. It is shown that these results are in good agreement with
neutron Compton scattering data for liquid water and ice.Comment: 4 page
Tunneling and delocalization in hydrogen bonded systems: a study in position and momentum space
Novel experimental and computational studies have uncovered the proton
momentum distribution in hydrogen bonded systems. In this work, we utilize
recently developed open path integral Car-Parrinello molecular dynamics
methodology in order to study the momentum distribution in phases of high
pressure ice. Some of these phases exhibit symmetric hydrogen bonds and quantum
tunneling. We find that the symmetric hydrogen bonded phase possesses a
narrowed momentum distribution as compared with a covalently bonded phase, in
agreement with recent experimental findings. The signatures of tunneling that
we observe are a narrowed distribution in the low-to-intermediate momentum
region, with a tail that extends to match the result of the covalently bonded
state. The transition to tunneling behavior shows similarity to features
observed in recent experiments performed on confined water. We corroborate our
ice simulations with a study of a particle in a model one-dimensional double
well potential that mimics some of the effects observed in bulk simulations.
The temperature dependence of the momentum distribution in the one-dimensional
model allows for the differentiation between ground state and mixed state
tunneling effects.Comment: 14 pages, 13 figure
Efficient multiple time scale molecular dynamics: using colored noise thermostats to stabilize resonances
Multiple time scale molecular dynamics enhances computational efficiency by
updating slow motions less frequently than fast motions. However, in practice
the largest outer time step possible is limited not by the physical forces but
by resonances between the fast and slow modes. In this paper we show that this
problem can be alleviated by using a simple colored noise thermostatting scheme
which selectively targets the high frequency modes in the system. For two
sample problems, flexible water and solvated alanine dipeptide, we demonstrate
that this allows the use of large outer time steps while still obtaining
accurate sampling and minimizing the perturbation of the dynamics. Furthermore,
this approach is shown to be comparable to constraining fast motions, thus
providing an alternative to molecular dynamics with constraints.Comment: accepted for publication by the Journal of Chemical Physic
Roughness of molecular property landscapes and its impact on modellability
In molecular discovery and drug design, structure-property relationships and
activity landscapes are often qualitatively or quantitatively analyzed to guide
the navigation of chemical space. The roughness (or smoothness) of these
molecular property landscapes is one of their most studied geometric
attributes, as it can characterize the presence of activity cliffs, with
rougher landscapes generally expected to pose tougher optimization challenges.
Here, we introduce a general, quantitative measure for describing the roughness
of molecular property landscapes. The proposed roughness index (ROGI) is
loosely inspired by the concept of fractal dimension and strongly correlates
with the out-of-sample error achieved by machine learning models on numerous
regression tasks.Comment: 17 pages, 6 figures, 2 tables (SI with 17 pages, 16 figures