[gmx-users] Harmonic dihedral restraints
bobjohnson1981 at gmail.com
Tue Feb 26 17:23:10 CET 2008
Thanks for your replies. How do you include these dihedral restraints
in the topology file? 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?
On Tue, Feb 26, 2008 at 1:15 AM, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Robert Johnson 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?
> A harmonic potential is just one where V is of the form you give above.
> However a dihedral angle (phi) is a circular variable, and so you need
> to take care not to have a huge potential resulting from the difference
> of 2pi+0.01 and zero - hence the "MOD 2pi". Delta-phi allows for your
> potential to be flat-bottomed with variable width; compare with distance
> restraints and Figure 4.13. Try plotting the function for various
> delta-phi to see what I mean (if it's not obvious). phi_0 is the angle
> about which the harmonic potential is applied, in the usual way.
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