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

Lianqing Zheng lzheng at me.rochester.edu
Thu Dec 7 18:24:33 CET 2006


Thanks a lot, Janne! I finally got it! Thanks for your inspiration! I
added 1-4 pairs in [pairs] and then got the right values. I thought
Gromacs would automatically find 1-4 pairs.

Lianqing

On Thu, 7 Dec 2006, Janne Hirvi wrote:

>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
>
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