[gmx-users] PLUMED Meeting 2017
das.sudip37 at gmail.com
Mon Feb 27 17:06:11 CET 2017
Sorry for spamming your inbox. I have unintentionally sent this mail.
On Mon, Feb 27, 2017 at 9:33 PM, Sudip Das <das.sudip37 at gmail.com> wrote:
> 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
>> 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
>> 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
>> enhanced-sampling methods have been developed in recent years. In
>> numerous analysis strategies have been developed to better exploit what
>> be learnt from short simulations.
>> Traditionally, ad-hoc implementations of these analysis and biasing
>> 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
>> lack of generalization. In addition, the various codes that have been
>> distributed, often use different conventions in their input files, which
>> confusing for end users. For these reasons we released a suite of analysis
>> and biasing routines called PLUMED (http://www.plumed.org) in 2009.
>> is an open source, freely-available plugin that can be interfaced with
>> 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
>> 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
>> 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
>> 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
>> 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
>> presented during the poster session.
>> It is not necessary to pay any fee for participation in either the
>> 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
>> 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
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