16 research outputs found
Sampling methods and free energy estimators for computer simulations: development and applications.
Implementations of nonequilibrium methods for free energy calculations: forthcoming developments of the ORAC molecular dynamics simulation code
IBIS2.0: The new Interferometric BIdimensional Spectrometer
We present the IBIS2.0 project, which aims to upgrade and to install the Interferometric BIdimensional Spectrometer at the solar Vacuum Tower Telescope (Tenerife, Spain) after its disassembling from the Dunn Solar Telescope (New Mexico, USA). The instrument is undergoing a hardware and software revision that will allow it to perform new spectropolarimetric measurements of the solar atmosphere at high spatial, spectral and temporal resolution in coordination with other ground- and space-based instruments. Here we present the new opto-mechanical layout and control system designed for the instrument, and describe future steps...
IBIS 2.0: optical layout and polarimetric unit of the Interferometric BIdimensional Spectrometer 2.0
Elastic Barrier Dynamical Freezing in Free Energy Calculations: A Way To Speed Up Nonequilibrium Molecular Dynamics Simulations by Orders of Magnitude
An important issue concerning computer
simulations addressed to
free energy estimates via nonequilibrium work theorems, such as the
Jarzynski equality [Phys.
Rev. Lett. 1997, 78, 2690], is the computational effort required to
achieve results with acceptable accuracy. In this respect, the dynamical
freezing approach [Phys.
Rev. E 2009, 80, 041124] has been shown to improve the efficiency of this kind
of simulations, by blocking the dynamics of particles located outside
an established mobility region. In this report, we show that dynamical
freezing produces a systematic spurious decrease of the particle density
inside the mobility region. As a consequence, the requirements to
apply nonequilibrium work theorems are only approximately met. Starting
from these considerations, we have developed a simulation scheme,
called “elastic barrier dynamical freezing”, according
to which a stiff potential-energy barrier is enforced at the boundaries
of the mobility region, preventing the particles from leaving this
region of space during the nonequilibrium trajectories. The method,
tested on the calculation of the distance-dependent free energy of
a dimer immersed into a Lennard-Jones fluid, provides an accuracy
comparable to the conventional steered molecular dynamics, with a
computational speedup exceeding a few orders of magnitude
Nonequilibrium Candidate Monte Carlo Simulations with Configurational Freezing Schemes
Nonequilibrium
Candidate Monte Carlo simulation [Nilmeier et al., <i>Proc. Natl.
Acad. Sci. U.S.A.</i> <b>2011</b>, <i>108</i>, E1009–E1018] is a tool devised to design Monte
Carlo moves with high acceptance probabilities that connect uncorrelated
configurations. Such moves are generated through nonequilibrium driven
dynamics, producing candidate configurations accepted with a Monte
Carlo-like criterion that preserves the equilibrium distribution.
The probability of accepting a candidate configuration as the next
sample in the Markov chain basically depends on the work performed
on the system during the nonequilibrium trajectory and increases with
decreasing such a work. It is thus strategically relevant to find
ways of producing nonequilibrium moves with low work, namely moves
where dissipation is as low as possible. This is the goal of our methodology,
in which we combine Nonequilibrium Candidate Monte Carlo with Configurational
Freezing schemes developed by Nicolini et al. (<i>J. Chem. Theory
Comput.</i> <b>2011</b>, <i>7</i>, 582–593).
The idea is to limit the configurational sampling to particles of
a well-established region of the simulation sample, namely the region
where dissipation occurs, while leaving fixed the other particles.
This allows to make the system relaxation faster around the region
perturbed by the finite-time switching move and hence to reduce the
dissipated work, eventually enhancing the probability of accepting
the generated move. Our combined approach enhances significantly configurational
sampling, as shown by the case of a bistable dimer immersed in a dense
fluid
Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework
The fast-switching
decoupling method is a powerful nonequilibrium
technique to compute absolute binding free energies of ligand–receptor
complexes (Sandberg et al., <i>J. Chem. Theory Comput</i>. <b>2014</b>, <i>11</i>, 423–435). Inspired
by the theory of noncovalent binding association of Gilson and co-workers
(<i>Biophys. J</i>. <b>1997</b>, <i>72</i>, 1047–1069), we develop two approaches, termed binded-domain
and single-point alchemical-path schemes (BiD-AP and SiP-AP), based
on the possibility of performing alchemical trajectories during which
the ligand is constrained to fixed positions relative to the receptor.
The BiD-AP scheme exploits a recent generalization of nonequilibrium
work theorems to estimate the free energy difference between the coupled
and uncoupled states of the ligand–receptor complex. With respect
to the fast-switching decoupling method without constraints, BiD-AP
prevents the ligand from leaving the binding site, but still requires
an estimate of the positional binding-site volume, which may not be
a simple task. On the other side, the SiP-AP scheme allows avoidance
of the calculation of the binding-site volume by introducing an additional
equilibrium simulation of ligand and receptor in the bound state.
In the companion article (DOI: 10.1021/acs.jctc.7b00595), we show
that the extra computational effort required by SiP-AP leads to a
significant improvement of accuracy in the free energy estimates