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.
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