[gmx-users] re:re:when using RB dihedral function, how to exclude 1-4 vdw ? (TJ Piggot)

XunJie Yang yangxunj at mail.ustc.edu.cn
Wed Dec 2 03:06:35 CET 2009

Tom wrote:
> If you read this part of the manual again you will see that it discusses 
> this point of 1-4 interactions for the OPLS forcefield and RB dihedrals 
> (and the same as discussed for OPLS is true for the AMBER forcefields using 
> RB  potentials for dihedrals).
> Tom

  Thanks very much for your comment, and excuse me for my late reply.
  I guess this method may not work, although the function form has been transformed to normal dihedral function, the calculated dihedral energy still includes 1-4 vdw(during the function transformation, calculated energy doesn't change). So in this case(when the dihedral paremeters are deduced from RB parameters), even we are using normal dihedral function(V=A(1+cos(nw+w0)), we still need to exclude 1-4 vdw.
  In fact, in GMX manual page 102, I found that 1-4 vdw is deduced from normal vdw, by multiplying a scaling factor(this scaling scheme is utilized by amber FF, but GMX force field doesn't treat 1-4 vdw by scaling), so I have changed this scaling factor of 1-4 vdw to 0.0, and found 1-4 vdw energy became 0 in the energy minimization output. This is how I exclude 1-4 vdw now, but I have not found any other users who posted that they have solved this problem in the same way, so I think I need to consult the mailing list further whether this solve is right or wrong.

Yang Xunjie
> --On Friday, November 20, 2009 16:45:44 +0800 XunJie Yang 
> <yangxunj at mail.ustc.edu.cn> 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!
> >
> > Yang Xunjie
> > 2009-11-20
> > --

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