[gmx-users] fudgeQQ (again ...)

Lianqing Zheng lzheng at me.rochester.edu
Wed Dec 6 17:22:57 CET 2006

Dear GMX-users,

Here are a followup and more details for my problem. I really hope to get
through this, so I can move on ...

I report the electrostatic energy (Uq, kJ/mol) for a molecule using 3

1. Gromacs 3.3
1 1 yes 0.5 FudgeQQ

FudgeQQ                  [moleculetype]               Uq
0.0, 0.8333, or 1.0       mol   3                    116.050
0.0, 0.8333, or 1.0       mol   2                   -413.048

2. DLPOLY with scaling factor of 0.83333
Uq = -324.68

3. My own code
Scaling factor   Uq
0.0            115.99
0.83333        -324.68
1.0            -412.81

Apparently, Gromacs gives the value without 1-4 interactions with "mol 3",
and the value for full 1-4 interactions with "mol 2", regardless of

Did I not do something right when using Gromacs?

Thanks A LOT for your help! BTW: the Gromacs website seems down.


On Wed, 29 Nov 2006, Lianqing Zheng wrote:

>Dear GMX-users,
>I'm doing normal mode analysis for one molecule and found the calculated
>electrostatic energy (at t=0) doesn't change at all regardless of the
>value for fudgeQQ. (I used "1 1 yes 0.5 0.83333" for [default] and
>"molecule 2" for [moleculetype].) If I use "molecule 3", the value will
>change but is still independent of fudgeQQ.
>Any idea what the problem is? I'll be happy to send you the input files if
>you need them. 
>Thanks a lot!
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