[gmx-users] wrong calculation of dihedral angle with angle restraint?

Tomas Kubar tomas.kubar at uochb.cas.cz
Wed Nov 23 18:07:11 CET 2005


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?


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