[gmx-users] Re: user-defined proper dihedrals and restraints

Chris O'Brien obrien at CLEMSON.EDU
Fri Oct 18 21:05:32 CEST 2002

>Chris O'Brien wrote:
> >
> > Hello,
> >
> > I have two questions.  First, is it possible to edit/create a user-defined
> > function for proper dihedrals?  My molecule (polylactic acid) is chiral, so
> > the dihedral rotation energy curve (phi vs theta) is not symmetric.  Thus,
> > a Ryckaert-Bellemans expression can never fit it properly.  It would need
> > phase shifts in the theta terms.  If this is possible, where in the program
> > would I need to make these additions?  Are there any pitfalls I should be
> > aware of?  If I were to make a piecewise (-180 to 0 and 0 to 180)
> > expression, do I need to worry about discontinuity or non-differentiability
> > at the junction?
>I'd say you should be able to do about anything you like in the current
>implementation, using either the R-B or simple sinoidal functions by
>defining a number of functions to the same atoms. That way you can get
>a sum of any number of (co)sine functions, phase shifted and/or with
>different multiplicities.

 From what I can gather, GROMACS only accepts C0, C1, ..., C5 as inputs for 
R-B dihedrals, which it uses to generate the energy function by a sum of 
cosine terms.  I don't see a way to input sine function R-B terms in 
addition to cosine terms (or equivalently, phase shift terms with just 
cosine) within GROMACS.  I guess this is the heart of my problem.  Without 
one or the other, the R-B will always be symmetric about 0 degrees.

Thank you,
Chris O'Brien

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