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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