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.

[1]  L Delle Site,et al.  Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling. , 2011, Physical chemistry chemical physics : PCCP.

[2]  William H Miller,et al.  Linearized semiclassical initial value time correlation functions using the thermal Gaussian approximation: applications to condensed phase systems. , 2007, The Journal of chemical physics.

[3]  Gregory A Voth,et al.  A comparative study of imaginary time path integral based methods for quantum dynamics. , 2006, The Journal of chemical physics.

[4]  Ericka Stricklin-Parker,et al.  Ann , 2005 .

[5]  Pep Español,et al.  Hamiltonian adaptive resolution simulation for molecular liquids. , 2012, Physical review letters.

[6]  L Delle Site,et al.  Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir. , 2011, Physical review letters.

[7]  Ian R. Craig,et al.  Quantum statistics and classical mechanics: real time correlation functions from ring polymer molecular dynamics. , 2004, The Journal of chemical physics.

[8]  Dominik Marx,et al.  On the applicability of centroid and ring polymer path integral molecular dynamics for vibrational spectroscopy. , 2009, The Journal of chemical physics.

[9]  L Delle Site,et al.  Quantum locality and equilibrium properties in low-temperature parahydrogen: a multiscale simulation study. , 2012, The Journal of chemical physics.

[10]  David E Manolopoulos,et al.  Comparison of path integral molecular dynamics methods for the infrared absorption spectrum of liquid water. , 2008, The Journal of chemical physics.

[11]  Carsten Hartmann,et al.  Molecular dynamics in a grand ensemble: Bergmann–Lebowitz model and adaptive resolution simulation , 2014, 1412.0866.

[12]  Victor V. Goldman,et al.  The isotropic intermolecular potential for H2 and D2 in the solid and gas phases , 1978 .

[13]  M. Tuckerman.  Statistical Mechanics: Theory and Molecular Simulation , 2010 .

[14]  Cecilia Clementi,et al.  Communication: On the locality of hydrogen bond networks at hydrophobic interfaces. , 2010, The Journal of chemical physics.

[15]  William H. Miller,et al.  Semiclassical theory of electronically nonadiabatic dynamics: results of a linearized approximation to the initial value representation , 1998 .

[16]  Michael J. Willatt,et al.  Communication: Relation of centroid molecular dynamics and ring-polymer molecular dynamics to exact quantum dynamics. , 2015, The Journal of chemical physics.

[17]  Francesco Paesani,et al.  Infrared and Raman Spectroscopy of Liquid Water through "First-Principles" Many-Body Molecular Dynamics. , 2015, Journal of chemical theory and computation.

[18]  Donald G Truhlar,et al.  Conservative Algorithm for an Adaptive Change of Resolution in Mixed Atomistic/Coarse-Grained Multiscale Simulations. , 2008, Journal of chemical theory and computation.

[19]  C.-E. A. WINs,et al.  Low , 2020, Definitions.

[20]  Terry Clark,et al.  Parallel Computing , 2017, Encyclopedia of GIS.

[21]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[22]  R. Feynman,et al.  Quantum Mechanics and Path Integrals , 1965 .

[23]  Christof Schütte,et al.  Chemical potential of liquids and mixtures via adaptive resolution simulation. , 2013, The Journal of chemical physics.

[24]  Alejandro Pérez,et al.  Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes. , 2011, The Journal of chemical physics.

[25]  Peter M. Kasson,et al.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit , 2013, Bioinform..

[26]  Michele Ceriotti,et al.  Efficient first-principles calculation of the quantum kinetic energy and momentum distribution of nuclei. , 2012, Physical review letters.

[27]  Abner Shimony,et al.  STATISTICAL MECHANICS OF OPEN SYSTEMS , 1962 .

[28]  Wei Zhang,et al.  An accurate and simple quantum model for liquid water. , 2006, The Journal of chemical physics.

[29]  Vijay S Pande,et al.  Finite domain simulations with adaptive boundaries: accurate potentials and nonequilibrium movesets. , 2013, The Journal of chemical physics.

[30]  Michael J. Willatt,et al.  Boltzmann-conserving classical dynamics in quantum time-correlation functions: "Matsubara dynamics". , 2015, The Journal of chemical physics.

[31]  Matej Praprotnik,et al.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution. , 2008, Annual review of physical chemistry.

[32]  David E. Manolopoulos,et al.  A refined ring polymer contraction scheme for systems with electrostatic interactions , 2008 .

[33]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[34]  Pierre-Nicholas Roy,et al.  Connection between the observable and centroid structural properties of a quantum fluid: application to liquid para-hydrogen. , 2004, The Journal of chemical physics.

[35]  Dominik Marx,et al.  Communications: On artificial frequency shifts in infrared spectra obtained from centroid molecular dynamics: Quantum liquid water. , 2010, The Journal of chemical physics.

[36]  Soonmin Jang,et al.  Applications of higher order composite factorization schemes in imaginary time path integral simulations , 2001 .

[37]  William H. Miller,et al.  Semiclassical approximations for the calculation of thermal rate constants for chemical reactions in complex molecular systems , 1998 .

[38]  D. Manolopoulos,et al.  An efficient ring polymer contraction scheme for imaginary time path integral simulations. , 2008, The Journal of chemical physics.

[39]  Soonmin Jang,et al.  Centroid molecular dynamics: A quantum dynamics method suitable for the parallel computer , 2000, Parallel Comput..

[40]  Peter G. Bergmann,et al.  Irreversible gibbsian ensembles , 1957 .

[41]  L Delle Site,et al.  Classical to path-integral adaptive resolution in molecular simulation: towards a smooth quantum-classical coupling. , 2010, Physical review letters.

[42]  Thomas F. Miller,et al.  Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics. , 2005, The Journal of chemical physics.

[43]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[44]  Alejandro Pérez,et al.  A comparative study of the centroid and ring-polymer molecular dynamics methods for approximating quantum time correlation functions from path integrals. , 2009, The Journal of chemical physics.

[45]  Animesh Agarwal,et al.  Path integral molecular dynamics within the grand canonical-like adaptive resolution technique: Simulation of liquid water. , 2015, The Journal of chemical physics.

[46]  Thomas E Markland,et al.  A fast path integral method for polarizable force fields. , 2009, The Journal of chemical physics.

[47]  William H Miller,et al.  Quantum dynamics of complex molecular systems. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[48]  Jianshu Cao,et al.  A new perspective on quantum time correlation functions , 1993 .

[49]  Thomas F. Miller,et al.  Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. , 2013, Annual review of physical chemistry.

[50]  Matej Praprotnik,et al.  Coupling different levels of resolution in molecular simulations. , 2009, The Journal of chemical physics.

[51]  Michele Parrinello,et al.  Efficient stochastic thermostatting of path integral molecular dynamics. , 2010, The Journal of chemical physics.

[52]  Luigi Delle Site,et al.  Formulation of Liouville's theorem for grand ensemble molecular simulations. , 2016, 1602.02031.

[53]  William H Miller,et al.  Including quantum effects in the dynamics of complex (i.e., large) molecular systems. , 2006, The Journal of chemical physics.

[54]  Peter G. Bergmann,et al.  New Approach to Nonequilibrium Processes , 1955 .

[55]  Michele Parrinello,et al.  Energy Conservation in Adaptive Hybrid Atomistic/Coarse-Grain Molecular Dynamics. , 2007, Journal of chemical theory and computation.

[56]  D. Manolopoulos,et al.  How to remove the spurious resonances from ring polymer molecular dynamics. , 2014, The Journal of chemical physics.

[57]  Rupert Klein.  Comments on “Open boundary molecular dynamics” by R. Delgado-Buscalioni, J. Sablić and M. Praprotnik , 2015 .