[gmx-users] Harmonic dihedral restraints

[David Mobley]

Bob,

The other way of putting what Mark said is that phi is only meaningful
on some range (-pi to pi, or 0 to 2pi, depending on how you define it)
and so what you require is that the potential be harmonic for the
region in which phi is meaningful. You don't care what happens outside
that. Or, in this case, you handle the issue by mapping phi values
outside the allowed range back into that allowed range.

David


On Mon, Feb 25, 2008 at 2:24 PM, Robert Johnson
<bobjohnson1981 at gmail.com> wrote:
> 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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