As per my previous post if you read this section more carefully you will
see that it mentions the use of RB dihedrals in combination with 1-4
interactions (and tells you not to modify topologies produced by pdb2gmx
for these cases!). You only need to exclude 1-4 interactions when using
RB's to simulate alkanes.
With regards to the scalings of the 1-4 VdW's, the fudge factor of 0.5 is
correct, as is the factor of 1/1.2 for the electrostatics (since the
AMBER-94 forcefield), and they should not be changed.
Hope this clarifies some points for you
Tom
--On Wednesday, December 02, 2009 10:49:16 +0800 XunJie Yang
<yangx...@mail.ustc.edu.cn> 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. 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? Thanks for your help!
Yang Xunjie
2009-12-2
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----------------------
TJ Piggot
t.pig...@bristol.ac.uk
University of Bristol, UK.
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