With this patch, dihedral_style helix now also obeys the IUPAC/IUB
sign convention shown in the figure posted earlier today
(and also here:
http://www.structuralbioinformatics.com/chapter7.shtml
http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.1b.html)
Change:
I only changed line 191 of dihedral_helix.cpp.
(dihedral_helix.h included as well, although it is unmodified.)
Testing:
The resulting behavior was tested using "test_system_dihedral.tar.gz"
(attached). The coefficients were chosen (A=B=0) so that 4-atom
system relaxes to an equilibrium whose dihedral angle is +135 degrees,
and whose dihedral energy decays down to zero.
If I get a chance to look at dihedral_style charmm and opls, I'll make
another post. Cheers.
Andrew
test_system_dihedral.tar.gz (3.32 KB)
dihedral_sign_convention.pdf (10.6 KB)
dihedral_helix.cpp (9.35 KB)
dihedral_helix.h (1.38 KB)