[gmx-users] analyzing protein conformation stability

Mark Abraham Mark.Abraham at anu.edu.au
Mon Oct 3 13:58:08 CEST 2011

On 03/10/11, *Sajad Ahrari * <sajadahrari at yahoo.com> wrote:
> Hello Dear users
> is there any command in gromacs for analysis of protein stability? or 
> I should be using those related to calculation of B-factor?

That's an extremely complex thing to attempt to measure. The observables 
in MD simulations are the positions and velocities of atoms. It is 
infeasible to simulate for long enough to measure something like the 
free energy of folding. You might be able to measure a relative 
stability using alchemical free energy methods, but that's not exactly a 
beginner topic.

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