[gmx-users] BCAM Internship Position Announcement

Bruno Escribano bescribano at bcamath.org
Thu May 22 18:07:19 CEST 2014

The following BCAM Internship position is open at BCAM – Basque Center for 
Applied Mathematics, an interdisciplinary research center located in Bilbao. 
The interested applicants can apply via the following webpage:
Research topic title:
Free energy calculations using molecular dynamics and Markov chain Monte Carlo 
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
Molecular Dynamics, Hybrid Monte Carlo, Umbrella sampling, Hamiltonian 
Required knowledge and skills:
Hamiltonian dynamics, Monte Carlo sampling, C programming, Unix/Linux
Required language skills:
Duration and dates:
2-3 months during 2014
Application deadline:
June 1st, 2014
Bruno Escribano and Elena Akhmatskaya
Research line:
Modelling and Simulation in Life and Materials Sciences - M3A Research Area
Bruno Escribano
BCAM Researcher
BCAM – Basque Center for Applied Mathematics
Alameda de Mazarredo, 14
E-48009 Bilbao - Basque Country - Spain
Tel. +34 946 567 853
bescribano at bcamath.org | www.bcamath.org
( matematika mugaz bestalde )

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