[gmx-users] Harmonic dihedral restraints
bobjohnson1981 at gmail.com
Mon Feb 25 23:24:33 CET 2008
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?
On Mon, Feb 25, 2008 at 2:47 PM, David Mobley <dmobley at gmail.com> wrote:
> 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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