[gmx-users] analyzing protein conformation stability
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
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