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

[Janne Hirvi]

Hello!

Just a simple question - Do you have [pairs]-section in your topology file?

Janne


> 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
> codes.
> 
> 1. Gromacs 3.3
> [default]
> 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
> fudgeQQ.
> 
> Did I not do something right when using Gromacs?
> 
> Thanks A LOT for your help! BTW: the Gromacs website seems down.
> 
> Lianqing
> 
> 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!
> >
> >Lianqing