Adaptive resolution simulation of polarizable supramolecular coarse-grained water models

Abstract

Anomalous viscosity effect in the early stages of the ion-assisted adhesion/fusion event between lipid bilayers: A theoretical and computational study The Journal of Chemical Physics 138, 234901 (2013) Multiscale simulations methods, such as adaptive resolution scheme, are becoming increasingly popular due to their significant computational advantages with respect to conventional atomistic simulations. For these kind of simulations, it is essential to develop accurate multiscale water models that can be used to solvate biophysical systems of interest. Recently, a 4-to-1 mapping was used to couple the bundled-simple point charge water with the MARTINI model. Here, we extend the supramolecular mapping to coarse-grained models with explicit charges. In particular, the two tested models are the polarizable water and big multiple water models associated with the MARTINI force field. As corresponding coarse-grained representations consist of several interaction sites, we couple orientational degrees of freedom of the atomistic and coarse-grained representations via a harmonic energy penalty term. This additional energy term aligns the dipole moments of both representations. We test this coupling by studying the system under applied static external electric field. We show that our approach leads to the correct reproduction of the relevant structural and dynamical properties. C 2015 Author(s). All article content, except where otherwise noted, is licensed under a Creative Commons Attribution 3.0 Unported License. [http://dx

Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution

“…In accordance with previous studies [51,58] we find that smoother NDPs are achieved when the TD forces are slightly extended into the AT and CG regions. Here, we apply the TD force in the range r AT −r skin < r < r HY +r skin , where r skin = 0.3 nm is the extension and r AT = 2.1 nm and r HY = 3.3 nm are the radii of the AT and HY domains, respectively.…”

“…Slight orientational ordering is observed at the AT/HY interface. This artifact, arising from the resolution change, was observed also in previous studies [25,38,58]. To further characterize the interactions between the DNA molecule and the solvent we investigate the hydrogen bonding between the DNA and water.…”

Quantum Mechanics/Molecular Mechanics Method Combined with Hybrid All-Atom and Coarse-Grained Model: Theory and Application on Redox Potential Calculations

“…To make comparison, the QM/AA/CG model was implemented on the basis of the all-atom TIP3P and coarse-grained PW or BMW water models, employing the hexaaquo metal complex as the QM subsystem and 515 TIP3P water molecules in a droplet of 15.5 Å radius with additional distance restraints (see below). The rest of systems were then four-to-one mapped to the polarizable supra-molecular coarse-grained waters [29]. All the systems were put in a cubic box of 64 × 64 × 64 Å 3 under periodic boundary conditions.…”

Simulation of macromolecular liquids with the adaptive resolution molecular dynamics technique

“…For chain lengths of 16 carbon atoms (hexadecane) or longer, the flexibility of the chains results in conformations, where the centers of mass of two entangled polymer chains can coincide ( Figure 6) and a coarse-grained representation using only one coarse-grained sphere becomes infeasible. A multibead coarse-grained model has been used in AdResS before to create a polarizable coarse-grained water model 29 . In contrast to the supermolecular water clusters modeled in that case, a bond in a coarse-grained model of a linear polymer would have to be mapped onto atomistic bonds during the transition, resulting in possible numerical instabilities.…”