Enhancing molecular simulations with PLUMED
- Gareth Tribello (Queen's University Belfast, United Kingdom)
- Giovanni Bussi (SISSA , Italy)
- Massimiliano Bonomi (University of Cambridge, United Kingdom)
- Davide Branduardi (Crucell Vaccine Institute, The Netherlands)
- Carlo Camilloni (University of Cambridge, United Kingdom)
Atomistic simulations play a fundamental and ever-increasing role in molecular biology, chemistry, and condensed-matter physics. Unfortunately, the large numbers of particles in realistic systems and the long ranged interactions between the atoms make simulations of biomolecules and technological materials computationally expensive. As a result direct simulation can only be used to examine process that occur on relatively short-time scales. The direct study of rare events such as protein folding, drug binding, chemical reactions and phase transitions is too much of a computational challenge in many cases of interest. To extend the time scales which can be investigated by atomistic simulations, several powerful enhanced-sampling methods have been developed in recent years. In addition, numerous analysis strategies have been developed to better exploit what can be learnt from short simulations.
Traditionally, ad-hoc implementations of these analysis and biasing methods have been written and used by their developers. In many cases these implementations have not been distributed to the wider community. Furthermore, they often reflect their developers’ interests and thus have a lack of generalization. In addition, the various codes that have been distributed, often use different conventions in their input files, which is confusing for end users. For these reasons we released a suite of analysis and biasing routines called PLUMED (http://www.plumed-code.org) in 2009. PLUMED is an open source, freely-available plugin that can be interfaced with some of the most popular molecular dynamics (MD) programs (GROMACS, NAMD, DL_POLY, AMBER, etc.). It allows the user to perform free-energy calculations using state-of-the-art enhanced sampling techniques, such as metadynamics, umbrella sampling, and steered MD. This unified and portable implementation of these enhanced sampling algorithms facilitates comparison between different techniques and between MD engines. In addition, PLUMED can be used to analyze trajectories both in post-processing and on-the-fly during the simulation.
PLUMED is developed and maintained by a team of researchers that includes the developers of some of the techniques described above as well as people who are actively working on the development of new enhanced sampling methods. PLUMED also benefits from the presence of over 200 active users in our mailing list. The feedback received from many of these users and conversations between the developers has recently led to PLUMED 2, a complete rewrite of the code in an object-oriented programming language (C++). This new version introduces greater flexibility and greater modularity, which makes it far easier to implement new methods and collective variables. As a result this new version moves the code towards a more community based project.
The aim of this tutorial is to showcase the functionalities that are available in PLUMED 2 in front of both users and developers and to thoroughly train participants on the practical use of the free-energy methods and novel analysis techniques that are implemented in the package. To do all of this we would opt for a slightly different strategy to other CeCAM tutorials. We would aim the first three days of the meeting at students with little to no experience of using these methods. During these days we will introduce these users to the fundamental statistical mechanical theories that underlie the free energy methods implemented in PLUMED through hands-on sessions that will train users to run calculations using PLUMED.
In the last three days of the meeting we would then run a user meeting to which will invite a few of researchers that actively used PLUMED in their own research. In addition, we will encourage the wider community to attend the meeting and present the work they are doing through both oral and poster presentations. One aim of this second part of the workshop is to show the participants in the workshop how these techniques are used in bleeding-edge research. This is particularly important as there are considerable differences between how these methods are applied to problems in different fields. It is thus important to show neophytes the basics of the methods and to present them with a range of more complex applications from a wide variety of different fields. Only then will they get a feel as to how to tackle real-life problems and on the sort of complex chemical/physical problems that can be studied using these methodologies.
The previous, CeCAM-sponsored PLUMED tutorial in 2010 and had over 80 applicants for only 35 places. In 2012 we organized a PLUMED meeting sponsored by SISSA that was also successful, with about 20 speakers and 50 participants. In addition, there have been at least two CeCAM workshops per year on free-energy methods, trajectory analysis or enhanced sampling for the past three years. We are thus confident that this will be a timely and successful activity.