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

[Janne Hirvi]

Hi!

I am not exactly sure but I think that there should be [pairs] section with all
pairs named and the function number (=1) included but without any parameters
which are then generated by Gromacs if "generate pairs" = "yes". You can check
from the .log -file if you have any 1-4 Coulombic (or 1-4 Lennard-Jones)
interactions included in your case. 

Janne


> Thanks, Janne!
> 
> No, I tried not having [pairs] or having empty [pairs] because the manual
> says it's not necessary if "generate pairs" = "yes".
> 
> Lianqing
> 
> 
> On Thu, 7 Dec 2006, Janne Hirvi wrote:
> 
> >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