XunJie Yang wrote:
hello GMX users:
  I am now using GMX together with FFamber, I found that the parameter files 
provided by FFamber uses RB functions (described in GMX manual p62) rather than 
normal dihedral function to calculate dihedral energy term. According to the 
manual(p62), when using RB function for dihedral angle, we should exclude 1-4 
vdw interactions because this interaction has been included in the RB 
calculation.

More precisely, you want GROMACS to do the calculation specified by the AMBER force field. What does this force field require for 1-4 VDW?

I have searched the FFamber homepage and found no comments or FAQ items about 
how to exclude 1-4 vdw and had to depend on myself, finally I found that, by 
changing the FudgeLJ variable in ffamber99.itp (the FF include file similar to 
ffgmx.itp) to 0.0, I successfully turn off the 1-4 vdw(as the 1-4 vdw energy in 
the EM result was zero). I am not much confident at what I did because the 
default value for FudgeLJ is 0.5 and is not 0.0, I just wonder why FFamber 
doesn't set FudgeLJ to 0.0, is it that they ignored this point? There must be 
many others using FFamber, so I want to know that, how do you solve this 
problem? Did you solve it the same way?

Once you've answered the above, I think your best approach is to email the maintainers of the AMBER ports.

Mark
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