A software pipeline for the rational design of soft materials
Trevor J. Jones1,2, Christoph Klein1,2, János Sallai,3 Christopher R. Iacovella1,2, Peter T. Cummings1,2, and Clare McCabe1,2,4
1) Department of Chemical and Biomolecular Engineering, 2)Vanderbilt Facility for Multiscale Modeling and Simulation (MuMS), 3) Institute for Software Integrated Systems, 4) Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
Spurred by the Materials Genome Initiative (MGI), there has been substantial effort to harness the power of supercomputing to accelerate the development of novel materials. Both the MIT Materials Project  and Harvard Clean Energy Project  have successfully leveraged molecular simulation to begin developing databases for crystalline structures and candidate molecules for organic electronic materials. However, to harness the power of molecular simulation on a scale required by the MGI for soft materials requires a different approach due to the added requirement of sampling systems in configurational space. To run automated, large-scale molecular dynamic simulations of arbitrary soft materials, system initialization is a current stumbling block. In order to use molecular dynamics for automated screening of soft material, a robust set of tools is required to automate the initialization of simulations in arbitrary chemical configurations and produce runnable input files for simulation engines.
Here, we present a suite of tools developed to create and parameterize such arbitrary systems and enable large scale parameter screening of soft materials. Although the biophysics simulation community has put considerable effort into developing software tools and databases for creating and parameterizing biological structures, these tools do not allow users to easily generate arbitrary structures. To this end, we have developed mBuild , a hierarchical component based molecular building tool that aims to simplify the constructions of complex initial configurations in a programmatic way to facilitate MGI screening. Users can then create parameterized input files for the GROMACS , LAMMPS , or Desmond , simulation engines by implicitly accessing foyer , an atomtyping and forcefield parameterization tool, and InterMol , a molecular dynamics input file conversion tool. We demonstrate the efficiency of using these tools by generating an ensemble of 42 alkylsilane and 42 polyethylene glycol monolayers attached to a silica substrate with varying surface densities and chain lengths in the matter of minutes on a conventional workstation. Adjusting the chemical composition in mBuild, such as the monomer length used, requires modification of a single argument, which can easily be embedded in a loop to facilitate screening. Simulations of the monolayers at steady state were performed using the GROMACS simulation engine to explore the nematic ordering of the systems and establish trends. The workflow presented here serves as a stepping stone towards the automated screening of soft materials using molecular simulation.
 A. Jain*, S.P. Ong*, G. Hautier, W. Chen, W.D. Richards, S. Dacek, S. Cholia, D. Gunter, D. Skinner, G. Ceder, K.A. Persson, "The Materials Project: A materials genome approach to accelerating materials innovation," APL Materials, 1(1), 011002. (2013)
 J. Hachmann, R. Olivares-Amaya, S. Atahan-Evrenk, C. Amador-Bedolla, R. S. Sánchez-Carrera, A. Gold-Parker, L. Vogt, A. M. Brockway, and A. Aspuru-Guzik, "The Harvard Clean Energy Project: Large-Scale Computational Screening and Design of Organic Photovoltaics on the World Community Grid," J. Phys. Chem. Lett., 2 (17), 2241–2251. (2011)
 C. Klein, J. Sallai, T. J. Jones, C. R. Iacovella, C. McCabe, and P. T. Cummings, "mBuild: A Hierarchical, Component Based Molecule Builder," (submitted)
 S. Pronk, S. Pall, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M. R. Shirts, J. C. Smith, P. M. Kasson, D. Van Der Spoel, B. Hess, E. Lindahl, "GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit." Bioinformatics 29, 845-854. (2013).
 S. Plimpton, "Fast Parallel Algorithms for Short-Range Molecular Dynamics," J Comp Phys, 117, 1-19 (1995).
 K. J. Bowers, E. Chow, H. Xu, R. O. Dror, M. P. Eastwood, B. A. Gregersen, J. L. Klepeis, I. Kolossvary, M. A. Moraes, F. D. Sacerdoti, J. K. Salmon, Y. Shan, and D. E. Shaw, “Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters,” Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), 11-17, (2006).
 foyer: an atomtyping and forcefield parameterization tool. Available at https://github.com/iModels/foyer.
 InterMol: a conversion tool for molecular dynamics simulations. Available at https://github.com/shirtsgroup/InterMol.
See more of this Group/Topical: Student Poster Sessions