[gmx-users] Re: fudgeQQ (again ...)
janne.hirvi at joensuu.fi
Thu Dec 7 08:30:24 CET 2006
Just a simple question - Do you have [pairs]-section in your topology file?
> 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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