[gmx-users] Re: gmx-users Digest, Vol 25, Issue 5

Erik Lindahl lindahl at sbc.su.se
Thu May 4 07:55:57 CEST 2006


On May 4, 2006, at 4:19 AM, gil claudio wrote:

> Thanks for the help, Erik and David.
> Does this mean that when invoking rb dihedrals, the
> real equation being used is
> RB(phi) = C0 - C1 cos(phi) + C2 cos^2(phi) - C3
> cos^3(phi) + C4 cos^4(phi) - C5 cos^5(phi)

Yes, if you convert it to biochemistry convention. In the code the  
angle is converted to polymer convention instead.
See equation 4.61, and note the following line where it says  

> It might be good to mention this convention in the
> manual.

I count at least three places where it is already mentioned in the  
section when we define RB-dihedrals and the conversion from OPLS  
parameters on pp 55-56, and an explicit note about the effect on the  
sign of C_n terms. ;-)



More information about the gromacs.org_gmx-users mailing list