[gmx-users] Harmonic dihedral restraints

[Robert Johnson]

Not sure if anyone saw this...I had a question about how to include
the dihedral restraints in the topology file. Unfortunately, this info
doesn't seem to be in the manual. There isn't a [ dihedral_restraints
] section listed in Table 5.4. I presume this section should be
formatted as:

[ dihedral_restraints ]
i     j     k     l     1     phi_0     k     delta_phi

Is that correct?

Thanks,
Bob

On Tue, Feb 26, 2008 at 11:37 AM, David Mobley <dmobley at gmail.com> wrote:
> 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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