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
--On Friday, November 20, 2009 16:45:44 +0800 XunJie Yang
<[email protected]> 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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TJ Piggot
[email protected]
University of Bristol, UK.
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