Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I
added 1-4 pairs in [pairs] and then got the right values. I thought
Gromacs would automatically find 1-4 pairs.
send the structure to pdb2gmx and the value of genpairs will be
determined from your ffXXX.itp file. As far as I know, this is only in
this way that the [pairs] section will be generated in the output.top
file. If your system is not a protein, then you need to add the paris
section (and in fact create the entire .top file) by hand.
By the way, why are you using the combination of genpairs=yes
fudgeLJ=0.5 and fudgeQQ=0.8333 ? This is not a valid combination for
any force field that comes in the standard gromacs distribution.
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