E-CAM Extended Software Development Workshop on Classical Molecular Dynamics

14 - 25 August 2017

Venue: Lorentz Center@Snellius

If you are invited or already registered for this workshop, you have received login details by email.

In the last few years modeling of rare events has seen tremendous progress, and several computational methods have been put forward to bridge the time scale gap. In particular, trajectory-sampling methods, such as transition path sampling, transition interface sampling, forward flux sampling promise an accurate yet efficient solution to the rare event problem in complex systems. However, these new approaches have not been included yet, with adequate efficiency and scalability, in common simulation packages, mostly because their application requires specialized expert knowledge.

The aim of this workshop is to discuss the implementation of the methods and create software modules that can be used in conjunction with existing MD codes to address the computational challenges caused by rare events. The ESDW2 workshop focuses on the development of user-friendly modules to sample rare barrier crossing trajectories and to analyze their molecular mechanisms. Participants will create python modules based on OpenPathSampling (OPS), a Python oriented framework for path sampling, around the OpenMM package. It will be thus mostly a ‘hands on’ workshop, with extended programming sessions, interspersed with basic and in-depth lectures. In particular, the focus will be on OPS-based modules for :

1.         Tools for obtaining initial paths

2.         Recently developed path sampling Monte Carlo moves

3.         Other rare events methods based on the path sampling framework

4.         Reweighting schemes

5.         Interface with external order parameter modules (e.g. PLUMED)

6.         Analysis tools for path ensembles

7.         High performance and parallelization

8.         Support for additional MD Engines (e.g. Gromacs, LAMMPS)

However, this is not an exclusive list, and participants are encouraged to bring in their own favorite application/module to develop. Of course, the topic should fit in the rare events framework.

Participants will be assigned projects at the start of the workshop to enable them to prepare knowledge of the background theory.  The assignment will be made on a consensual basis taking into account the participants’ interests and experience. Participants will also be provided with an overview of the software tools to be used (provided by E-CAM).


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