Grand-Canonical Adaptive Resolution Centroid Molecular Dynamics: Implementation and application

نویسندگان

  • Animesh Agarwal
  • Luigi Delle Site
چکیده

We have implemented the Centroid Molecular Dynamics scheme (CMD) into the Grand Canonical-like version of the Adaptive Resolution SimulationMolecular Dynamics (GC-AdResS) method. We have tested the implementation on twodifferent 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 degrees of freedom required for a given

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

Grand-canonical-like molecular-dynamics simulations by using an adaptive-resolution technique

In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive resolution simulation (AdResS) technique in sampling the Grand Canonical ensemble. We demonstrate that the correct density and radial distribution functions in the hybrid region, where molecules change resolution, are two necessary conditions for considering the atomistic a...

متن کامل

Adaptive Resolution Simulation (AdResS): A Smooth Thermodynamic and Structural Transition from Atomistic to Coarse Grained Resolution and Vice Versa in a Grand Canonical Fashion.

The AdResS method in molecular dynamics (MD) allows, in a grand canonical (GC) fashion, to change on-the-fly the number of degrees of freedom of a system, allowing to pass from atomistic (AT) to coarse-grained (CG) resolution and vice versa as a function of the position of the molecule in the simulation box. The coupling of resolutions is made in a thermodynamically consistent way, though in th...

متن کامل

Enabling grand-canonical Monte Carlo: Extending the flexibility of GROMACS through the GromPy python interface module

We report on a python interface to the GROMACS molecular simulation package, GromPy (available at https://github.com/GromPy). This application programming interface (API) uses the ctypes python module that allows function calls to shared libraries, for example, written in C. To the best of our knowledge, this is the first reported interface to the GROMACS library that uses direct library calls....

متن کامل

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 above mentioned limitation implies t...

متن کامل

Molecular dynamics in a grand ensemble: Bergmann–Lebowitz model and adaptive resolution simulation

This article deals with themolecular dynamics simulation of open systems that can exchange energy andmatter with a reservoir; the physics of the reservoir and its interactions with the system are described by themodel introduced by Bergmann and Lebowitz (PGBergmann and J L Lebowitz 1955 Phys. Rev. 99 578). Despite its conceptual appeal, themodel did not gain popularity in thefield of molecular ...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Computer Physics Communications

دوره 206  شماره 

صفحات  -

تاریخ انتشار 2016