[gmx-developers] request to join a development project

servaas michielssens servaas.michielssens at student.kuleuven.be
Wed May 7 09:23:59 CEST 2008

Dear Gromacs developers,

I am a PhD student at the computational chemistry group of the University of 
Leuven. I started molecular dynamics in my master thesis using the amber 
package. I switched to Gromacs when I started my PhD (november2007).
The reason I address you is that I would like to gain some experience in 
developing molecular dynamics code. Since our group is relative new to 
molecular dynamics, I believe it could be a valuable experience to join a 
project in a lab with tradition in this area. I wonder if any of your labs 
has a proposal for such a project (for 1 or 2 months, e.g. a project form 
the wiki pages) in wich I can learn and cooperate at the development of 
Gromacs. By this I hope to learn more about the Gromacs code, meeting people 
who develop Gromacs and to contribute to the development of Gromacs.
I included some information on my previous and current work. I am especially 
interested in the replica exchange method and its variants.

Thanks in advance,

Servaas Michielssens

Previous work on the fluorescent protein Dronpa:

S. L. C. Moors, S. Michielssens, C. Flors, P. Dedecker, J. Hofkens and A. 
Ceulemans, How do mutants control the cis-trans isomerization of Dronpa: a 
replica exchange molecular dynamics study, J. Chem. Theor. Comput. 

Current project:

In progress:
-Docking to HIV-RT using replica exchange with solute tempering
(in gromacs with small modification in repl_ex.c and md.c)
-Quantum chemistry of phosphoramidate hydrolysis

-QM/MM of phosphoramidate hydrolysis in HIV-RT
-Using transition interface sampling to determine mechanism and rate 
constant of open-close transition in the hand domain of reverse 
transcriptase (in cooperation with Dr. van Erp). 

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