[gmx-users] Request for dihedral PMF test system or complete alanine dipeptide topology file

[David Mobley]

Chris,

> >Right. I remember looking into this at one point, and I don't think
> >the manual is correct; it looks to me like dihres.c handles
> >periodicity properly. In particular, there is the followign comment in
> >dihres.c:
>
> It's good to see that this is actually a comment in the source code, I didn't look there.
> Perhaps the manual should be updated?

That would be a good idea. Developers?

> >I assume you're clear on the fact that the phi and dphi are in degrees
> >but the force constants aren't? And your units are otherwise correct?
> >(i.e. you're remembering output is in kJ/mol?)
>
> I use phi in degrees and always use dphi=0
> For wham I convert my force constant to kcal/mol/deg^2 by multiplying the fc value like this:
> # 500 kJ/mol/rad^2 * 1rad^2/3282.8063485deg^2 * 1kcal/4.184kJ= 0.0364026 kcal/mol/deg^2

Good deal. I always found it confusing that you have to specify the
angle in degrees but the force constant in radians, but it looks like
you've got it right...

David