[gmx-users] For FFamber, should FudgeLJ variable in ffamber.itp be 0.0?

TJ Piggot t.piggot at bristol.ac.uk
Wed Dec 2 17:59:09 CET 2009

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


--On Wednesday, December 02, 2009 10:49:16 +0800 XunJie Yang 
<yangxunj at 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.piggot at bristol.ac.uk
University of Bristol, UK.

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