HPC @UPV/EHU

The following BCAM Internship position is open at BCAM – Basque Center for Applied Mathematics, an interdisciplinary research center located in Bilbao.  The research topic is free energy calculations using molecular dynamics and Monte Carlo methods. The interested applicants can apply via the following web page:

http://www.bcamath.org/en/research/internships

Internship data

Research topic title

Free energy calculations using molecular dynamics and Markov chain Monte Carlo methods.

Research topic description

Study, implementation and testing of Monte Carlo techniques combined with classical molecular dynamics (MD) with the ultimate objective of calculating protein binding energies ΔG. The project will result in a new simulation method based on the adaptation of the existing Generalized Shadow Hybrid Monte Carlo (GSHMC) to umbrella sampling. The tasks to be performed by the intern involve:

• Modifying the open-source software MD package GROMACS.

• Setting up and running simulations of biomolecular systems using the modified software on parallel computational servers.

• Analysing results and calculating ΔG using the potential of mean force curve.

Keywords

Molecular Dynamics, Hybrid Monte Carlo, Umbrella sampling, Hamiltonian dynamics.

Required knowledge and skills

Hamiltonian dynamics, Monte Carlo sampling, C programming, Unix/Linux.

Required language skills

English.

Duration and dates

2-3 months during 2014.

Application deadline

June 1st, 2014.

Supervisors

Bruno Escribano and Elena Akhmatskaya.

Research line

Modelling and Simulation in Life and Materials Sciences – M3A Research Area.

General