Quick question for clarification:
For the charmm dihedral style, does LAMMPS consider 0 or 180 as trans?
Thanks
Most (hopefully all) dihedral styles in LAMMPS obey a convention where
the trans-state corresponds to a dihedral angle of 180 degrees. For
details, see:
http://lammps.sandia.gov/doc/dihedral_style.html
There is a possible exception for dihedral_style "quartic" (part of
USER-MISC), which Sally Bridgewater pointed out uses a different
convention. She posted a fix for this (and I promised to and then
forgot to test this fix). I don't know if that fix ended up in
LAMMPS. For details see:
http://sourceforge.net/mailarchive/message.php?msg_id=31227618
Cheers
Andrew
more details:
I personally tested that dihedral_styles
charm
fourier
table
class2
cosine/shift/exp
helix
(and fix restrain)
...all obey the "IUPAC/IUB" dihedral-angle convention.
(with the trans angle at 180 degrees)
angle sign convention here:
http://kinemage.biochem.duke.edu/teaching/anatax/images/fig006.72.png
http://kinemage.biochem.duke.edu/teaching/anatax/html/anatax.1b.html
http://lammps.sandia.gov/doc/Eqs/dihedral_sign.jpg
I don't think I ever tested harmonic, multi/harmonic, opls, nharmonic,
or quadratic. Sally Bridgewater posted a bug report on "quadratic".
(not "quartic") In any case, I hope that fix got added. (and I
apologize for not following up on that.)
http://sourceforge.net/mailarchive/message.php?msg_id=31227618
cheers
andrew