[gmx-users] the total charge of system is not an integer

[Mark Abraham]

On 5/04/2011 3:57 PM, ahmet yıldırım wrote:
> Dear Tsjerk,
>
>     Hi Ahmet,
>
>     As suggested, it's better to break up your molecule into smaller
>     charge groups. Note that charge groups don't need to have zero charge,
>     nor integer charge. In your case, I'd suggest two COH groups for EDO,
>     which will have zero net charge each, and for TRS I'd take the COH
>     groups as separate charge groups. I also note that the COH groups,
>     although chemically identical - H3NC(COH)3, right?-, have different
>     charges. That doesn't seem proper.
>
>     Hope it helps,
>
>     Tsjerk
>
>
> nonrevised .itp file:
> EDO      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OA     1  EDO     OAB     1   -0.111  15.9994
>      2         H     1  EDO     HAE     1    0.031   1.0080
>      3       CH2     1  EDO     CAA     1    0.080  14.0270
>      4       CH2     1  EDO     CAC     1    0.080  14.0270
>      5        OA     1  EDO     OAD     1   -0.111  15.9994
>      6         H     1  EDO     HAF     1    0.031   1.0080
>
> nonrevised .itp file:
> EDO      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OA     1  EDO     OAB     1   -0.111  15.9994
>      2         H     1  EDO     HAE     1    0.031   1.0080
>      3       CH2     1  EDO     CAA     1 *0.000*  14.0270
>      4       CH2     1  EDO     CAC     1 *0.000*  14.0270
>      5        OA     1  EDO     OAD     1   -0.111  15.9994
>      6         H     1  EDO     HAF     1    0.031   1.0080
>
> can you show me on the itp file? how do I seperate two COH groups? 
> Please help me

We didn't say to use zero *charges*. We said you need small charge 
groups. Since EDO is neutral, then by symmetry each half must also be 
neutral.

Have a look at the way charge groups are used in the .rtp file for your 
forcefield. You need to do similar things. If you don't understand the 
file formats yet, you need to read up on chapter 5 of the manual.

Mark
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