[gmx-developers] Possible bug in grompp?

[Walter Ash]

I've been working on a new molecule topology and I've noticed what I 
believe is a bug in grompp...  I am using the ffopls forcefield with 
genpairs=yes, fudgeQQ and fudgeLJ = 0.5,  and combination rule 3.  This 
is with the 3.2.1 distribution version.

In the molecular topology, under [ pairs ], it appears I have to specify 
LJ14 parameters in C6 and C12 format despite the use of sigma and 
epsilon everywhere else in this forcefield (comb rule 3).  If I use 
sigma and epsilon in a [ pairs ] definition, my LJ14 energies are orders 
of magnitude too high as grompp intereprets these parameters as C6 and 
C12 values instead.  Putting C6 and C12 parameters here gives the 
expected behavior.

This is contrary to what is stated in the manual and what I would expect 
the behavior to be.