[gmx-users] Using "pairs" type 2

[Liel Sapir]

Hey all,

I have been reading many post about this issue, but still do not have a
clear answer.

I am using the AMBER force-field where 1-4 interactions are scaled (fudgeLJ
= 0.5 and fudgeQQ = 0.8333).
In addition I use parameters of molecules that require the 1-4 interaction
to NOT be scaled.

What I did to solve this issue is the follwoing: In the molecules *itp file
I listed all 1-4 interactions explicitly. I used the pairs type 2, as in
here:

[ pairs ]
1 14 2 1 0.161 0.175 0.339967 0.457730

As you can see, I use fudgeQQ=1, with the "Real" charges, and the needed LJ
parameters.

I think this works properly, and that it is equivalent (for the molecule of
interest) to use "type 1" with no explicit parameters (that will be
accordingly generated from ffnonbonded.itp), along with a forcefield.itp
that sets the fudge factors to 1.0.

What worries me is that the manual says "type 2" is used for free energy
simulations and TI.
Can I still use it as mentioned above? Am I missing something?

Thanks much,

Liel