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

[Lianqing Zheng]

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
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