[gmx-users] Several general questions about correctness of molecular modeling

[Иванов Миша]

Dear Gromacs users,

I would like to know the following things about molecular dynamics:

1) What RMSD value, obtained in molecular dynamics as a function of time, is believed to be normal? I received, that after 1 ns of simulation RMSD value augmented up to 2 A for backbone atoms. It seems for me very large.

2) Whether molecular dynamics should reproduce a B-factor of protein residues, obtained experimentally in X-ray analysis. I received in MD that B-factor for side chains of protein residues is sufficiently bigger then that from X-ray structure.

3) What minimal time is needed to perform a molecular dynamics of a protein in water? How the time, required for equilibration, should be determined? Is it sufficient to see, that Potential energy reached a plateau, and all the trajectory after this time can be used for analysis?

Thank you in advance.
Misha Ivanov