ARCHER Webinar: Mulit-resolution modelling of biological systems in LAMMPS

Multi-resolution modelling of biological systems in LAMMPS
Iain Bethune and Oliver Henrich
Two recent ARCHER eCSE projects (eCSE04-07 and eCSE05-10) have implemented extensions to LAMMPS to allow efficient simulations of biological systems using multiscale or dual-resolution coarse-grained/atomistic approaches.
The first project concerns the implementation of ELBA, an ELectrostatics-BAsed force-field originally designed for modelling lipid bilayers, but which is also transferrable to applications like computation of solvation free energies of biomolecules in water. Simulations using ELBA may combine coarse-grained beads with atomistic particles described using standard force-fields, for example membrane proteins embedded in a bilayer. We will discuss the implementation of a new integration algorithm for stable long-timescale Molecular Dynamics, and extensions to the LAMMPS load balancer to improve parallel performance in dual-resolution simulations.
The second project implemented the oxDNA force field, a coarse-grained model for nucleic acids. New pair interactions have been developed and permit now dynamical simulation of single and double stranded DNA on very large time and length scales. LAMMPS has emerged as a suitable computational platform for coarse-grained modelling of DNA and this eCSE project created a possibility to compare and optimise them with a view towards later multiscale modelling of DNA. We will explain how the oxDNA force field is parametrised and discuss a set of new Langevin-type rigid body integrators with improved stability.

[andrewjewett]

There are now tools to prepare LAMMPS simulations with both with ELBA and oxDNA. See the links below:

There's also a growing list of other coarse grained LAMMPS models here:
Disclaimer: Currently, the ELBA example only includes the ELBA water model (a dipole), but more complicated molecules containing bonded dipoles and bonded ellipsoids should be possible as new capabilities are added to LAMMPS. (Such as the upcoming "USER-MOLC" package.)
For more information, visit:
(Disclaimer: I wrote moltemplate.)
Hi.