[gmx-users] when using RB dihedral function, how to exclude 1-4 vdw ?

Mark Abraham Mark.Abraham at anu.edu.au
Fri Nov 20 10:11:47 CET 2009

XunJie Yang wrote:
> Hello GMX users:
>   I'm new to GMX and I'm now facing a problem. For short, it is about how to properly use the RB function.
>   I'm now doing simulation with AMBER force field(ported to GMX by FFAmber), which employs Ryckaert-Bellemans function for dihedral, it is how FFAmber forcefield treats dihedral angles as the parameters provided are only for RB function. 
>   According to GMX Manual page 62, using RB function implies exclusion of 1-4 LJ interactions between the first and last atom of the dihedral, which means, I should turn off the 1-4 vdw term while retaining the 1-4 coulomb term. However, I haven't found the way of doing so. If I deleted the [pairs] block in the topology file, all 1-4 interactions including 1-4 coulomb interaction would be deleted.
>   Could anyone who knows key to this problem give me some help? Thanks in advance!

Why are you needing an R-B function when using AMBER? If you're 
introducing something from another force field, that's a bad idea. See 
http://www.gromacs.org/Documentation/Terminology/Force_Fields and links 


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