95 research outputs found
Adaptive Resolution Simulation in Equilibrium and Beyond
In this paper, we investigate the equilibrium statistical properties of both
the force and potential interpolations of adaptive resolution simulation
(AdResS) under the theoretical framework of grand-canonical like AdResS
(GC-AdResS). The thermodynamic relations between the higher and lower
resolutions are derived by considering the absence of fundamental conservation
laws in mechanics for both branches of AdResS. In order to investigate the
applicability of AdResS method in studying the properties beyond the
equilibrium, we demonstrate the accuracy of AdResS in computing the dynamical
properties in two numerical examples: The velocity auto-correlation of pure
water and the conformational relaxation of alanine dipeptide dissolved in
water. Theoretical and technical open questions of the AdResS method are
discussed in the end of the paper
Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and Application
We have implemented the Centroid Molecular Dynamics scheme (CMD) into the
Grand Canonical-like version of the Adaptive Resolution Simulation Molecular
Dynamics (GC-AdResS) method. We have tested the implementation on two different
systems, liquid parahydrogen at extreme thermodynamic conditions and liquid
water at ambient conditions; the reproduction of structural as well as
dynamical results of reference systems are highly satisfactory. The capability
of performing GC-AdResS CMD simulations allows for the treatment of a system
characterized by some quantum features and open boundaries. This latter
characteristic not only is of computational convenience, allowing for
equivalent results of much larger and computationally more expensive systems,
but also suggests a tool of analysis so far not explored, that is the
unambiguous identification of the essential (quantum) degrees of freedom
required for a given property
Chemical potential of liquids and mixtures via Adaptive Resolution Simulation
We employ the adaptive resolution approach AdResS, in its recently developed
Grand Canonical-like version (GC-AdResS) [Wang et al. Phys.Rev.X 3, 011018
(2013)], to calculate the excess chemical potential, , of various
liquids and mixtures. We compare our results with those obtained from full
atomistic simulations using the technique of thermodynamic integration and show
a satisfactory agreement. In GC-AdResS the procedure to calculate
corresponds to the process of standard initial equilibration of the system;
this implies that, independently of the specific aim of the study, ,
for each molecular species, is automatically calculated every time a GC-AdResS
simulation is performed.Comment: 16 pages, 6 figures, 1 tabl
Simulation of liquid water
Quantum effects due to the spatial delocalization of light atoms are treated
in molecular simulation via the path integral technique. Among several
methods, Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful
tool to investigate properties induced by spatial delocalization of atoms;
however, computationally this technique is very demanding. The above mentioned
limitation implies the restriction of PIMD applications to relatively small
systems and short time scales. One of the possible solutions to overcome size
and time limitation is to introduce PIMD algorithms into the Adaptive
Resolution Simulation Scheme (AdResS). AdResS requires a relatively small
region treated at path integral level and embeds it into a large molecular
reservoir consisting of generic spherical coarse grained molecules. It was
previously shown that the realization of the idea above, at a simple level,
produced reasonable results for toy systems or simple/test systems like liquid
parahydrogen. Encouraged by previous results, in this paper, we show the
simulation of liquid water at room conditions where AdResS, in its latest and
more accurate Grand-Canonical-like version (GC-AdResS), is merged with two of
the most relevant PIMD techniques available in the literature. The comparison
of our results with those reported in the literature and/or with those
obtained from full PIMD simulations shows a highly satisfactory agreement
Molecular Dynamics in a Grand Ensemble: Bergmann-Lebowitz model and Adaptive Resolution Simulation
This article deals with the molecular dynamics simulation of open systems
that can exchange energy and matter with a reservoir; the physics of the
reservoir and its interactions with the system are described by the model
introduced by Bergmann and Lebowitz.Despite its conceptual appeal, the model
did not gain popularity in the field of molecular simulation and, as a
consequence, did not play a role in the development of open system molecular
simulation techniques, even though it can provide the conceptual legitimation
of simulation techniques that mimic open systems. We shall demonstrate that the
model can serve as a tool to devise both numerical procedures and conceptual
definitions of physical quantities that cannot be defined in a straightforward
way by systems with a fixed number of molecules. In particular, we discuss the
utility of the Bergmann-Lebowitz (BL) model for the calculation of equilibrium
time correlation functions within the Grand Canonical Adaptive Resolution
method (GC-AdResS) and report numerical results for the case of liquid water.Comment: 31 pages, 6 figure
Path Integral Molecular Dynamics within the Grand Canonical-like Adaptive Resolution Technique: Simulation of Liquid Water
Quantum effects due to the spatial delocalization of light atoms are treated
in molecular simulation via the path integral technique. Among several methods,
Path Integral (PI) Molecular Dynamics (MD) is nowadays a powerful tool to
investigate properties induced by spatial delocalization of atoms; however
computationally this technique is very demanding. The abovementioned limitation
implies the restriction of PIMD applications to relatively small systems and
short time scales. One possible solution to overcome size and time limitation
is to introduce PIMD algorithms into the Adaptive Resolution Simulation Scheme
(AdResS). AdResS requires a relatively small region treated at path integral
level and embeds it into a large molecular reservoir consisting of generic
spherical coarse grained molecules. It was previously shown that the
realization of the idea above, at a simple level, produced reasonable results
for toy systems or simple/test systems like liquid parahydrogen. Encouraged by
previous results, in this paper we show the simulation of liquid water at room
conditions where AdResS, in its latest and more accurate Grand-Canonical-like
version (GC-AdResS), is merged with two of the most relevant PIMD techniques
available in literature. The comparison of our results with those reported in
literature and/or with those obtained from full PIMD simulations shows a highly
satisfactory agreement
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