Extended Software Development Workshop: Trajectory Sampling
CECAM-AT, Traunkirchen, Austria
During the the past decades, classical MD simulation has become a central tool in many branches of science and engineering. In particular, in molecular biology, chemistry and materials science, MD simulations now routinely provide insights into molecular mechanisms with a spatial and temporal resolution not accessible to experimental probes.While several software packages for MD simulations have been developed, opening the possibility to carry out such simulations to a broad community of researchers, the relatively short time scales accessible to MD simulations still limit the applicability of MD, particularly to processes dominated by rare but important barrier crossing events such as protein folding, chemical reactions in solution and nucleation phenomena. The goal of the ESDW is to create software modules that can be used in conjunction with existing programs to address the computational challenges caused by rare events. In particular, we will focus on the development of user-friendly modules to sample rare barrier crossing trajectories and to analyse their molecular mechanisms.
Up to twelve junior participants (mainly PhD students and postdocs) will take part in the workshop, which will start with introductory lectures on the goals of the workshop and the required scientific background given by the senior researchers of ECAM. This introduction will include also lectures on development guidelines and software engineering. The participants will then form work groups of 2-3 people and start work on specific software modules (see below). Each day of the workshop will be concluded by a documentation of the progress made.
The main goal of the workshop is the creation of a library of python modules for path sampling and analysis. In particular, the following modules will be developed with the help of the participants of the first ESDW:
·Basic shooting and shifting algorithm
·Biased path sampling
·Aimless shooting algorithm
·Reactive flux algorithm
·Calculation of the transition state ensemble
·Maximum likelihood optimization of the reaction coordinate
The modules to be developed will be interfaced with the OpenMM toolkit for high performance molecular simulations, which is available as open source code. OpenMM provides an efficient library of routines central for molecular simulation including the implementation of optimized forces fields, routines for building complex biomolecular and materials systems as well as molecular dynamics integrators for various statistical mechanical ensembles. What makes OpenMM particularly powerful as a molecular dynamics engine underlying the path sampling and analysis modules of WP1 is that it is extremely flexible and guarantees high performance through optimization on all common GPU platforms.
Christoph Dellago (University of Vienna) - Organiser
Gerhard Kahl (Institut für Theoretische Physik, TU Wien) - Organiser & speaker