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

Christoph Freudenberger christoph.freudenberger at chemie.uni-ulm.de
Mon Oct 21 09:12:28 CEST 2002

Chris O'Brien wrote:
>> > 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.
I think you didn't get Anton right. What he suggested was to define
a couple of periodic and/or R-B functions on the same quartet of atoms.
The resulting pontential function will be the sum of all these functions.
See the gnuplot i attached as example.
The sum of the two functions remains continous and differentable at 
-180/180 deg.

Christoph Freudenberger
Abt. Organische Chemie I AK Siehl - Uni Ulm -Tel: ++49-731-502-2785
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