[gmx-users] getting started-protein folding

Justin A. Lemkul jalemkul at vt.edu
Thu Jan 22 16:45:03 CET 2009

dota wrote:
> Hi.I have recently installed Gromacs-3.3.3. & I want to study protein 
> folding on a small protein.Where should I get more information about 
> protein folding in Gromacs, what has been done up until now & how was it 
> done(except the manual)? I tried but I didn’t find a lot.What kind of 
> force field it is used? I found that implicit models are not suggested 
> for Gromacs. What about coarse-grained models? Can I use such models in 
> Gromacs?Or an all-atom model should be used?I found smth about the 
> MARTINI model in studies of more complex protein-lipids models. But what 
> about trying to fold a single peptide on a reasonable time-scale? I am 
> trying to find a way to get started..Any advice would be apreciated.Thanks!

There is no substitute for a thorough literature search using general terms like 
"protein folding and Gromacs."  Replica exchange MD may be a useful tool.  As 
for force fields, that is up to you to decide based on what you read.

Also, upgrade to the newest version of Gromacs (4.0.3), it is substantially 
faster than 3.3.3 and will help you gather more data much more quickly!


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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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