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
therein.
Mark
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