ESDW: Topics in Classical MD

Classical molecular dynamics (MD) is a broad field, with many domains of expertise. Those specialist domains include topics like transition path sampling (which harvests many examples of a process in order to study it at a statistical level [1]), metadynamics (which runs a trajectory with modified dynamics that enhance sampling, and from which free energy profiles can be constructed [2]), as well as various topics focused on the underlying dynamics, either by providing better representations of the interactions between atoms (e.g., force fields [3] or neural network potentials [4]) or by changing the way the dynamics are performed (e.g., integrators [5]). <br> <br>Frequently, experts in one domain are not experienced with the software of other domains. This workshop aims to combine both depth, by extending domain-specific software, and breadth, by providing participants an opportunity to learn about software from other domains. As an extended software development workshop (ESDW), a key component of the workshop will be the development of modules that extend existing software packages. Ideally, some modules may connect multiple domain-specific packages. <br> <br>Topics at this workshop will include using and extending modern MD software in the domains of: <br> <br>* advanced path sampling methods (and the software package OpenPathSampling) <br>* metadynamics and the calculation of collective variables (and the software package PLUMED) <br>* machine learning for molecular dynamics simulatons (including local structure recognition and representation of potential energy surfaces) <br> <br>In addition, this workshop will feature an emphasis on performance testing and benchmarking software, with particular focus on high performance computing. This subject is relevant to all specialist domains. <br> <br>By combining introductions to software from different specialist fields with an opportunity to extend domain-specific software, this workshop is intended to provide opportunities for cross-pollination between domains that often develop independently. <br> <br>References <br>[1] Bolhuis, P.G. and Dellago, C. Trajectory‐Based Rare Event Simulations. Reviews in Computational Chemistry, 27, p. 111 (2010). <br>[2] A. Laio and F.L. Gervasio. Rep. Prog. Phys. 71, 126601 (2008). <br>[3] J.A. Maier, C. Martinez, K. Kasavajhala, L. Wickstrom, K.E. Hauser, and C. Simmerling. J. Chem. Theory. Comput. 11, 3696 (2015). <br>[4] T. Morawietz, A. Singraber, C. Dellago, and J. Behler. Proc. Natl. Acad. Sci USA, 113, 8368 (2016). <br>[5] B. Leimkuhler and C. Matthews. Appl. Math. Res. Express, 2013, 34 (2013).