Pilot Project on the development of the GC-AdResS scheme

Dr. Christian Krekeler

Host beneficiary: Freie Universität Berlin, Department for Mathematics and Informatics, Germany

Industrial partner: MODAL AG, Germany

 

Description

Grand Canonical Adaptive Resolution Scheme (GC-AdResS) is getting more  recognition throughout the scientific community. The main aspect is to couple two simulation boxes together and combine the advantages of classical atomistic simulations with those from coarse gained simulations. The goal of the pilot project is to develop a library or recipe with which GC-AdResS can be implemented in any MD Code. Our current focus is adjusting the implemented Version of GC-AdResS in GROMACS. The long-term goal of this project is to promote and stimulate the community to use it as a tool for multiscale simulations and Analysis.

For question on how to adjust the code and those interested to use GC-AdResS, don't hesitate to contact me: ch.krekeler@fu-berlin.de

Development Plan

List of Tasks

  • Set up a new scheme in GROMACS (in the Moment Version 5.1.0) and adjust the Fallout in the form of adjusting the thermodynamic force interpolation
  • Set up a new scheme in ESPRESSO++ in cooperation with the Developers in Mainz
  • And finally generalizing those schemes

List of Modules

Modules: 

  1. Several Tools for Analysis 
  2. Manual
  3. First scheme for GROMACS 

Status:  in Preparation

Expected delivery date: Nov 2017

Description: Since we work mostly conceptually...the given titles are self-explaining

Published Results

List of publications:

B. Shadrack Jabes, C. Krekeler, R. Klein, L. Delle Site, "Probing Spatial Locality in Ionic Liquids with the Grand Canonical Adaptive Resolution Molecular Dynamics Technique", submitted to JCP October 2017 (invited issue)

Luigi Delle Site, "Grand Canonical Adaptive Resolution Simulation for Molecules with Electrons: A Theoretical Framework based on Physical Consistency " , Computer Physics Communications (2017) in press
http://arxiv.org/abs/1709.08452

Luigi Delle Site, Giovanni Ciccotti and Carsten Hartmann, "Partitioning a macroscopic system into independent subsystems " , J. Stat. Mech. Theor. Exp. 083201 (2017)
Open Access

 Luigi Delle Site and Matej Praprotnik, "Molecular systems with open boundaries: Theory and Simulation " , Physics Reports 693, 1-56 (2017)
Open access

Animesh Agarwal, Cecilia Clementi and Luigi Delle Site, "Path Integral-GC-AdResS simulation of a large hydrophobic solute in water: A tool to investigate the interplay between local microscopic structures and quantum delocalization of atoms in space " , Phys.Chem.Chem.Phys. 19,13030-13037 (2017)
C7CP01629H

Christoph Junghans, Animesh Agarwal and Luigi Delle Site, "Computational Efficiency and Amdahl's law for the Adaptive Resolution Simulation Technique " , Computer Physics Communications, 215, 20 (2017)
cpc.2017.01.030

Christian Krekeler and Luigi Delle Site, "Towards Open Boundary Molecular Dynamics Simulation of Ionic Liquids " , Phys.Chem.Chem.Phys 19, 4701 (2017)
C6CP07489
Featured in Advances in ENGINEERING

 

Outreach Material