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

David spoel at xray.bmc.uu.se
Wed Nov 16 20:09:06 CET 2005

On Wed, 2005-11-16 at 21:55 +0300, Иванов Миша wrote:
> 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.
Depends on the size of your protein. Try it for e.g. individual helices.
> 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.
This is quite common too and does not have to be bad, but you have to
justify the results...

> 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?
Difficult, different per protein etc. Check literature.

> Thank you in advance.
> Misha Ivanov
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel

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