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

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....

Boltzmann bias grand canonical Monte Carlo.

We derive an efficient method for the insertion of structured particles in grand canonical Monte Carlo simulations of adsorption in very confining geometries. We extend this method to path integral simulations and use it to calculate the isotherm of adsorption of hydrogen isotopes in narrow carbon nanotubes (two-dimensional confinement) and slit pores (one-dimensional confinement) at the temper...

Grand canonical Monte Carlo simulations of water in protein environments.

The grand canonical simulation algorithm is considered as a general methodology to sample the configuration of water molecules confined within protein environments. First, the probability distribution of the number of water molecules and their configuration in a region of interest for biochemical simulations, such as the active site of a protein, is derived by considering a finite subvolume in ...

Parallel Grand Canonical Monte Carlo (ParaGrandMC) Simulation Code

Pivot-coupled grand canonical Monte Carlo method for ring simulations

A new method is presented for the simulation of an ensemble of polymer rings of variable size at fixed monomer chemical potential. Called pivot-coupled grand canonical Monte Carlo ~PC-GCMC!, it is based on the directed addition or removal of a monomer to or from a ring, coupled to the pivot of a section of the ring to maintain the ring’s continuity. Application of PC-GCMC to single, isolated ri...