[gmx-users] Urey bradley term in the sum of energies

[Mark Abraham]

Nicolas SAPAY wrote:
> Hello everybody,
> 
> I've got an awful doubt on how the Urey-Bradley (UB) term is taken into
> account in the potential energy. When an angle has got regular and UB
> parameters, how this will appear in the .edr file?

If you have a force field with both angle function 1 and angle function 
5 (IIRC, for U-B) defined for the same set of 3 atoms, then to the best 
of my knowledge, GROMACS will do both blithely and the output will go 
into "Angles" and "U-B" in the expected fashion. Certainly this happens 
when such functions are defined for different sets of 3 atoms. Note that 
from GROMACS point of view, the U-B term includes both the angle stretch 
and the harmonic position stretch. CHARMM the program lists only the 
latter as U-B.

> The angle energy will
> only appear in the UB term only or it will be splitted between Angle and
> UB terms? I guess that both parameters are used in the computation but I'm
> not sure whether they are added before be printed in the .edr file or not.

I'm not quite sure what you're asking, but the structure of the bonded 
interaction code is such that all of the angle functions of type 1 will 
contribute only to "Angles" and all of the angle functions of type 5 
will contribute only to "U-B".

Mark