[gmx-users] Harmonic dihedral restraints

Robert Johnson 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.
>  Mark
> _______________________________________________
>  gmx-users mailing list    gmx-users at gromacs.org
>  http://www.gromacs.org/mailman/listinfo/gmx-users
>  Please search the archive at http://www.gromacs.org/search before posting!
>  Please don't post (un)subscribe requests to the list. Use the
>  www interface or send it to gmx-users-request at gromacs.org.
>  Can't post? Read http://www.gromacs.org/mailing_lists/users.php

More information about the gromacs.org_gmx-users mailing list