[gmx-users] Harmonic dihedral restraints

David Mobley 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?
>  Thanks,
>  Bob
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