[gmx-users] rigid body again

David van der Spoel spoel at xray.bmc.uu.se
Thu Jun 9 16:30:37 CEST 2005

On Thu, 2005-06-09 at 10:19 -0400, Lianqing Zheng wrote:
> Dear gmxers,
> I have checked the archive and it seems gmx is not directly supporting
> rigid molecule simulation. I'm wondering if the following will work.
> Say, for a molecule of N atoms, we choose 3N-6 independent internal
> coordinates (e.g., from a Z-matrix) and constrain all these bonds (by
> [constraints]), angles (by all-angles), and dihedrals (by adding 
> improper dihedrals with large force constants). Will this achieve a rigid
> molecule? Did anyone have any experience in this?
large force constants will make high-frequency vibration forcing you to
use very short time steps. Try adding long range constraints instead,
but be careful that it may be difficult to solve for the constraints
unless they are very accurately defined (distances). You may even need
double precision.
> Thanks a lot for your help!
> Lianqing
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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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