[gmx-users] artificial stabilization of helical content

David van der Spoel spoel at xray.bmc.uu.se
Mon Nov 29 17:22:41 CET 2004

On Mon, 2004-11-29 at 10:06 -0600, Germana Paterlini wrote:
> The AMBER force field (PARM96) is known for overestimating the helical
> conformation.
> Corrections have been made by modifying the phi/psi dihedral
> potentials.
> What is the behavior of GROMOS96 with respect to the helical
> conformation?
> When comparing simulations with experimental data (i.e CD), what %
> error one should expect (10%, 30%)?
> I am assuming that artifacts from PME periodicity have been
> eliminated.
If you ask Wilfred van Gunsteren (the developer of the GROMOS
forcefield) he will say that CD spectra can be reproduced by the gromos
force field for peptides at least, but that they do not contain any
structural information.

For helices it may be a bit different. However, you are stacking
uncertainties, because the calculation of the rotational strength is
difficult and error prone. So when you have bad results it may be force
field or the calculation of the CD spectrum, when you have good results
it may be compensation of errors.
> Thanks
> Germana Paterlini
> Germana Paterlini, Ph.D.
> Certusoft, Inc.
> Minneapolis, MN 55439
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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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