135 research outputs found
Single molecule pulling with large time steps
Recently, we presented a generalisation of the Jarzynski non-equilibrium work
theorem for phase space mappings. The formalism shows that one can determine
free energy differences from approximate trajectories obtained from molecular
dynamics simulations in which very large timesteps are used. In this work we
test the method by simulating the force induced unfolding of a deca-alanine
helix in vacuum. The excellent agreement between results obtained with a small,
conservative time step of 0.5 fs and results obtained with a time step of 3.2
fs (i.e., close to the stability limit) indicates that the large time step
approach is practical for such complex biomolecules. We further adapt the
method of Hummer and Szabo for the simulation of single-molecule force
spectroscopy experiments to the large time step method. While trajectories
generated with large steps are approximate and may be unphysical - in the
simulations presented here we observe a violation of the equipartition theorem
- the computed free energies are exact in principle. In terms of efficiency,
the optimum time step for the unfolding simulations lies in the range 1-3 fs.Comment: 8 pages, 8 figure
Theoretical prediction of the homogeneous ice nucleation rate: disentangling thermodynamics and kinetics
Estimating the homogeneous ice nucleation rate from undercooled liquid water
is at the same time crucial for understanding many important physical phenomena
and technological applications, and challenging for both experiments and
theory. From a theoretical point of view, difficulties arise due to the long
time scales required, as well as the numerous nucleation pathways involved to
form ice nuclei with different stacking disorders. We computed the homogeneous
ice nucleation rate at a physically relevant undercooling for a single-site
water model, taking into account the diffuse nature of ice-water interfaces,
stacking disorders in ice nuclei, and the addition rate of particles to the
critical nucleus.We disentangled and investigated the relative importance of
all the terms, including interfacial free energy, entropic contributions and
the kinetic prefactor, that contribute to the overall nucleation rate.There has
been a long-standing discrepancy for the predicted homogeneous ice nucleation
rates, and our estimate is faster by 9 orders of magnitude compared with
previous literature values. Breaking down the problem into segments and
considering each term carefully can help us understand where the discrepancy
may come from and how to systematically improve the existing computational
methods
Accurate determination of crystal structures based on averaged local bond order parameters
Local bond order parameters based on spherical harmonics, also known as
Steinhardt order parameters, are often used to determine crystal structures in
molecular simulations. Here we propose a modification of this method in which
the complex bond order vectors are averaged over the first neighbor shell of a
given particle and the particle itself. As demonstrated using soft particle
systems, this averaging procedure considerably improves the accuracy with which
different crystal structures can be distinguished
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