ProtoMD: A prototyping toolkit for multiscale molecular dynamics

Abstract

ProtoMD is a toolkit that facilitates the development of algorithms for multiscale molecular dynamics (MD) simulations. It is designed for multiscale methods which capture the dynamic transfer of information across multiple spatial scales, such as the atomic to the mesoscopic scale, via coevolving microscopic and coarse-grained (CG) variables. ProtoMD can be also be used to Licensing provisions: GPL v3 (or above)Programming language: python 2.7.3Computer: x86 / x86 64Operating system: Linux RAM: Depends on the size of the system being simulated and duration of the simulation (few MBs to TBs)Number of processors used: 12 -128Supplementary material:Keywords: python, molecular dynamics, multiscale, coarse-graining Classification:Computational Methods External routines/libraries:GROMACS, MDAnalysis, GromacsWrapper, numpy, scipySubprograms used:Nature of problem:Prototyping multiscale coarse-grained algorithms for molecular dynamics Solution method:Combining the open-source GROMACS molecular dynamics package and the pythonbased MDAnalysis library for running, debugging, and analyzing multiscale simulations Restrictions:The system under study must be characterized by a clear separation of timescales; otherwise, the multiscale algorithm fails to capture the slowly-varying modes. Unusual features:Additional comments:Running time:Depending on the problem size, simulations can take few hours to months.

Real-Time Interactive Modeling and Simulation in Biological Physics and Active Matter with Mechanica

“…The first and foremost requirement of any simulation software is the ability to actually represent, model, simulate and analyze things in the problem domain. In previous papers, we have made a series of studies in what are the core mechanisms in active matter and biological physics [29,28,26,25,24]. We have identified the core physical concepts or mechanisms that we believe can serve as a basis set of fundamental building blocks with which to construct biological and active matter simulations.…”

Multiscale Computation: Needs and Opportunities for BER Science

“…In cases where the systems are not far from equilibrium so that the nonlinear effects are negligible, and various length scales are sufficiently different for processes at two or more consecutive scales to be separable, a dual (Fig. 1) or multiple continuum approach 1,11,12 can be used to more accurately model the impact of sub-grid scale variability for reactive multiphase flow and transport. In this approach, the pore fluid is partitioned into flowing and stagnant domains.…”

“…To advance the field of multiscale theory and computation, the implementation is in two distinct forms. For the MD type calculations, the protoMD software is developed for researchers with interests in proposing and testing multiscale algorithms [12]. In contrast, the DMS package folds all the multiscale techniques directly into the GROMACS packages to achieve optimal computations efficiency by avoiding writing and reading files.…”

Temporally Coarse-Grained All-Atom Molecular Dynamics Achieved via Stochastic Padé Approximants

“…An additional problem is an I/ O computational overhead resulting from interaction of traditional and multiscale MD computational engines which was resolved by implementing the deductive multiscale part within a traditional MD source code. 69,73 Another deductive approach developed earlier is multiscale factorization which uses a coevolution operator formalism for coevolving the CG and atom-resolved variables and its approximation via Trotter factorization. 74,75 This provides an efficient simulation algorithm for constructing a single atomresolved trajectory and illustrates the interplay of CG and atom-resolved variables.…”