[gmx-users] Folding simulation using gromacs

[Mirco Wahab]

On 01.10.2014 03:52, AINUN NIZAR M wrote:
> I'm a newbie in MD. I would like to simulate a protein folding, from a
> primary protein structure to a fully-folded state  for a wild type and
> mutated protein. Then I will compare them and make movie from unfolded to
> folded state. I want to use REMD method. I want to know the system free
> energy as well. Can i do it with gromacs?

You can try that and it will "work" if you set it up correctly.
Will the results be of any use? Probably not. This is, actually,
a very complicated topic which requires a lot work up front.

For the start - don't miss this recent article in PLOS on the
topic from the Perutz-Lab (Vienna) - they use Gromacs.
=> 
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003638

Regards

M.