[gmx-users] Harmonic dihedral restraints

[Robert Johnson]

Hello everyone,
I am trying to calculate the absolute free energy of binding between a
DNA base and a nanotube. To do this, I am first calculating the free
energy associated with restraining the base in the correct binding
geometry in accordance with Boresch et. al. J. Phs. Chem. B., 107,
2003. In this paper, all restraints (1 distance, 2 angles, 3
dihedrals) are assumed to be harmonic. In Gromacs, there already
exists a harmonic distance restraint. Technically, the angle restraint
(Equation 4.67 in the manual) is not harmonic. However, for small
angle displacements it can be approximated as harmonic, so that's not
a problem either.

However, there is no harmonic dihedral restraint. A reasonable
solution would be to use an improper dihedral (Equation 4. 59 in the
manual) for the restraint. Is this alright, or are there any problems
that could arise from using this? To my knowledge, exclusions are
defined by bonds. Thus, I don't think I have to worry about the
improper dihedral affecting the exclusions. Is this correct?

Thanks,
Bob