[gmx-users] Harmonic dihedral restraints
dmobley at gmail.com
Mon Feb 25 20:47:18 CET 2008
I am not sure which manual you are looking at, but in the GROMACS 3.3
manual, equation 4.70 gives the dihedral restraint as harmonic.
On Mon, Feb 25, 2008 at 10:10 AM, Robert Johnson
<bobjohnson1981 at gmail.com> wrote:
> 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?
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