[gmx-users] wrong calculation of dihedral angle with angle restraint?
spoel at xray.bmc.uu.se
Wed Nov 23 19:25:36 CET 2005
On Wed, 2005-11-23 at 18:07 +0100, Tomas Kubar wrote:
> I'm trying to restrain a dihedral angle (i-j-k-l) to -24 deg. In the
> course of the simulation, the structure of my molecule gets distorted
> rapidly and the simulation itself crashes with segfault; it seems that
> the function low_angres() in src/gmxlib/bondfree.c calculates the
> dihedral angle in a wrong way - only as the angle of vectors ij and kl.
> This angle differs from the definition of a dihedral angle (maybe it
> even lies in the interval 0-180 deg) and consequently, the desired value
> is not reached.
> Do you think my interpretation is right?
do you use angle restraint or dihedral restraints? For the latter I have
just committed a fix to CVS which will be in 3.3.1
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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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