Archive for March, 2011

Molecular modelling of matter course

March 23rd, 2011


BCAM is organizing a course on Molecular Modelling of Matter.

Molecular modeling of matter:

what can we do now, and in the near future?

28 March – 1 April 2011 from 11:00 to 13:00
Bizkaia Technology Park, Building 500
E-48160 Derio (Spain)
Telephone +34 946 567 842

This course will provide an introduction to modeling at the electronic, atomistic and meso-scales of matter. Computational quantum mechanical methods, with some emphasis on density functional theory, will be discussed in the beginning of the course, followed by a more detailed treatment of molecular simulation methods (molecular dynamics and Monte Carlo) based on numerical solution of the equations of semi-classical statistical


Prof. Keith Gubbins and Prof. Jesús M. Ugalde


  1. Quantum mechanical methods. Introduction, Hartree-Fock approximation, electron correlation, density functional theory. [Prof. Ugalde]
  2. Introduction to atomistic simulation methods. Molecular dynamics simulation methods. Finite difference algorithms. Constraint molecular dynamics. [Prof. Gubbins]
  3. 3. Semi-classical statistical mechanics. Canonical, Microcanonical and Grand Canonical ensembles. Monte Carlo method, Canonical ensemble. [Prof. Gubbins]
  4. Monte Carlo method in the Grand Canonical and Isobaric ensembles. [Prof. Gubbins]
  5. Coarse graining and meso-scale methods. Lattice Monte Carlo. Brownian dynamics. Dissipative particle dynamics. [Prof. Gubbins]

More details



Workshop de AMBER en Barcelona

March 16th, 2011

AMBER is a family of force fields and programs for molecular dynamics of biomolecules. Amber Workshop 2011 that will be held in Barcelona from the 3rd to 6th May. The course will be taught by Ross C. Walker and Adrian E. Roitberg and will be hosted by the IRB Barcelona and the Barcelona Supercomputing Center.

AMBER MD Workshop 2011

May 3-6, Barcelona.
Limited number of seats. You will be requested to fill a pre-registration form before the 1st of April.
Workshop web page.
AMBER web page


Classes will be held from Tuesday 3rd to Friday 6th of May, starting at 9:00 AM to 6:00 PM, with breaks for lunch and coffee. List of covered topics:

  1. Introduction to force fields and molecular dynamics (Lecture).
  2. Overview of AMBER and it’s programs (Lecture).
  3. Introduction to setting up and running simulations (Lecture / Hands on).
  4. Visualizing AMBER simulations (Hands on).
  5. Overview of AMBER Force Fields / Solvent Models etc. (Lecture).
  6. Introduction to implicit solvent and binding energy calculations (Lecture).
  7. Protein folding and advanced analysis (Hands on).
  8. Simulating Sugars and the Glycam Force Field (Lecture / Hands on).
  9. Designing good simulation projects (Lecture).
  10. Dealing with non-standard residues (Lecture / Hands on).
  11. What to do if there is no crystal structure (Lecture).
  12. Statistical mechanics for free energy calculations.[Thermodynamic Integration] (Lecture / Hands on).
  13. QM/MM coupled potential simulations (Lecture).
  14. GPU accelerated MD (Lecture).


Análisis de mapas e información geoespacial con MATLAB

March 10th, 2011


Seminario online

.Este webinario muestra las principales funcionalidades de la herramienta Mapping Toolbox entre las que se incluye la creación de mapas, acceso al servicio Web Map (WMS), análisis de datos de terreno y simulaciones numéricas.
Además veremos herramientas complementarias para aplicaciones geoespaciales, como Image Processing Toolbox y Parallel Computing Toolbox.

Mostraremos la funcionalidades clave para el análisis de mapas, siguiendo esta agenda:

  • Introducción a Mapping Toolbox.
  • Simulación de vertido petrolífero, creación de mapas y simulación numérica.
  • Evitación meteorológica: WMS, procesado de imagen, cálculos geográficos, navegación.
  • Análisis de terreno: modelos de elevación digital, visionado de superficies.
  • Toolboxes relacionadas.
  • Preguntas y respuestas.
  • Cubre los siguientes productos.
  • Mapping Toolbox.
  • Image Processing Toolbox.
  • Parallel Computing Toolbox.


16 mar 2011 a las 16:00 hora local.

Duración 1 hora.

Más información y registrarse aquí.