On 03/10/11, *Sajad Ahrari * <[email protected]> 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.
Mark
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