[gmx-users] BCAM Internship Position Announcement

[Bruno Escribano]

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:
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
 
Supervisor:
Bruno Escribano and Elena Akhmatskaya
 
Research line:
Modelling and Simulation in Life and Materials Sciences - M3A Research Area
 
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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 )