[gmx-users] PLUMED Meeting 2017

Sudip Das das.sudip37 at gmail.com
Mon Feb 27 17:03:08 CET 2017

Dear Tarakda,

As CCEM meeting is from 15th to 20th May, should I attend this PLUMED
meeting also (22-27th May)? What do you suggest? Yet I haven't talk to sir
regarding this.


On Mon, Feb 27, 2017 at 9:11 PM, Giovanni Bussi <bussi at sissa.it> wrote:

> Dear all,
> this meeting might be relevant for gromacs users, so we also post it here.
> Atomistic simulations play a fundamental and ever-increasing role in
> biophysics, 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.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.
> On May 22-27, 2017 we are organizing a PLUMED meeting at the Scuola
> Internazionale di Studi Avanzati (SISSA), Trieste, Italy. The format will
> be similar to the meeting held in Belfast, UK, in 2014, that is three days
> of introductory tutorial followed by a three day user meeting. The tutorial
> will start on Monday 22 in the morning and finish on the afternoon of
> Wednesday 24. The user meeting will start on the morning of Thursday 25 and
> finish at lunchtime on Saturday 27.
> There are a limited number of places for students and post-docs that wish
> to join the meeting. We expect two types of participants:
>    - Students who wish to participate in both the tutorial and the user
>    meeting
>    - More senior participants who wish to only take part in the user
> meeting
> We invite all participants to submit an abstract. We will select the
> participants who will present talks during the user meeting from the
> abstracts submitted. Those abstracts that are not accepted for talks can be
> presented during the poster session.
> It is not necessary to pay any fee for participation in either the tutorial
> or the user meeting. However, we will only be able to pay for the
> accommodation of those speakers presenting talks at the user meeting.
> Furthermore, we will only be able to support three nights (Wednesday to
> Saturday) of accommodation for these speakers.  We will not be able to
> provide any financial or logistical support for your trip to Trieste.
> *The deadline for applications is March 15.* Those candidates admitted to
> the tutorial, to the user meeting, or selected to give an oral
> presenteation will be notified by the April 1, so as to have time to
> organize their trip.
> All the information, including the application form, can be found at
> http://sites.google.com/view/plumed-meeting-2017/home
> Hoping to see you in Trieste,
> Giovanni, Max, Carlo, and Gareth
> --
> Giovanni Bussi
> Scuola Internazionale Superiore di Studi Avanzati - SISSA
> via Bonomea 265, 34136 Trieste, Italy
> email: bussi at sissa.it
> web:   http://people.sissa.it/~bussi
>           http://srnas.sissa.it
> --
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