[gmx-users] Harmonic dihedral restraints

[Robert Johnson]

Well, the potential is of the form V=k(x1-x2)^2, but I don't see how
it's harmonic. What you would want is the x1 and x2 to refer to
dihedral angles. However, the potential in equation 4.70 has this
weird phi-phi_0 MOD 2pi term and this delta_phi parameter. It's just
not obvious to me how equation 4.70 can be expanded or rearranged to
look like a harmonic potential in the dihedral angles. Am I just not
seeing something correctly?
Bob


On Mon, Feb 25, 2008 at 2:47 PM, David Mobley <dmobley at gmail.com> wrote:
> Robert,
>
>  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.
>
>  David
>
>
>
>
>  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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