[gmx-users] Folding simulation using gromacs

Mirco Wahab mirco.wahab at chemie.tu-freiberg.de
Wed Oct 1 12:32:40 CEST 2014

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.



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