[gmx-users] protein melting experiment by GROMACS

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 30 03:22:47 CEST 2012

Acoot Brett wrote:
> Dear All,
> I remember before I have read a something on melting the protein from a 
> predefined starting temperature to a predefined end temperature by MD, 
> so that after the MD we can look at the whole process to see which part 
> of the protein unfold earlier, which part of the protein of the protein 
> unfold earlier. No I cannot find that introduction.
> After we equilibriate the protein system, will you please tell me how to 
> define the temperature gradient from the start temperature to the end 
> temperature in the mdp file? Or do you have a protocol on it?

See the manual regarding simulated annealing.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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