[AMBER] PLUMED Meeting 2017

From: Giovanni Bussi <giovanni.bussi.gmail.com>
Date: Tue, 14 Feb 2017 10:03:01 +0100

Dear all,

this meeting might be relevant for amber 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
   - 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
Hoping to see you in Trieste,

Giovanni, Max, Carlo, and Gareth
AMBER mailing list
Received on Tue Feb 14 2017 - 01:30:02 PST
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