[gmx-users] Harmonic dihedral restraints

[Justin A. Lemkul]

Quoting Robert Johnson <bobjohnson1981 at gmail.com>:

> 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

I've never done this before, but I recall a discussion about dihedral restraints
not too long ago.  There is some detailed information on the Wiki:

http://wiki.gromacs.org/index.php/Dihedral_Restraints

Maybe it will be of use.

-Justin

>
> 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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========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

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