[gmx-users] Re: A strange phenomenon in the new version opls-aa force field
lindahl at csb.stanford.edu
Fri Oct 10 17:51:02 CEST 2003
> I noted that you have changed the cetral atoms(N or C) from the
> position 1 to the position 3.
> I think the atom order of the old version is correct. Becuase in the
> opls-aa force field, we use
> proper dihedrals [1+cos(2*x+180)] to model improper dihedrals. The
> improper torsion angle should be
> defined as the angle between planes(C, CA, +N) and (CA,+N,O). But inn
> the new version *.rtp file, the
> impropers section define the angle between planes(CA,+N,C) and
> Why you changed the atom order for improper torsion? Could you give me
> detail explanation?
Because that's the way they are defined in OPLS & Amber - there really
isn't any right/wrong choice - both of them will work :-)
To the first order the potentials will be the same, but in second order
they differ slightly depending on the order (which changes the
definition of the planes). All the improper potentials are only
order-of-magnitude guesses, though, so it doesn't matter...
In the long run I want to have them identical to Amber/OPLS to
facilitate comparisons, but you can change it back without risking any
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