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

[Mark Abraham]

On 5/04/2011 9:59 PM, ahmet yıldırım wrote:
> Dear Mark,
>
> Now, are the files correct?

They're well-formed, but you've not taken Tsjerk's advice and arranged 
for (COH)3(NH3+)C to have charges consistent with its symmetry. When 
people donate their time to you, please use it or demonstrate why you 
shouldn't :-)

Mark

> *EDO.itp*:
> [ moleculetype ]
> ; Name nrexcl
> 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 *2*    0.080  14.0270
>      5        OA     1  EDO     OAD *2*   -0.111  15.9994
>      6         H       1  EDO     HAF *2 *   0.031   1.0080
>
> *TRS.itp:*
> [ moleculetype ]
> ; Name nrexcl
> TRS      3
>
> [ atoms ]
> ;   nr      type  resnr resid  atom  cgnr   charge     mass
>      1        OA     1  TRS      O1     1   -0.119  15.9994
>      2         H     1  TRS      H13     1    0.032   1.0080
>      3       CH2     1  TRS      C1     1    0.087  14.0270
>      4      CCl4     1  TRS        C *3*    0.055  12.0110
>      5       CH2     1  TRS      C3 *4 *   0.049  14.0270
>      6        OA     1  TRS      O3 *4*   -0.205  15.9994
>      7         H     1  TRS      H33 *4*    0.019   1.0080
>      8        NL     1  TRS         N *5*    0.206  14.0067
>      9         H     1  TRS         H2 *5*    0.004   1.0080
>     10         H     1  TRS        H3 *5*    0.004   1.0080
>     11         H     1  TRS        H1 *5 *  0.004   1.0080
>     12       CH2     1  TRS      C2 *6 *   0.150  14.0270
>     13        OA     1  TRS      O2 *6*   -0.205  15.9994
>     14         H     1  TRS      H23 *6*    0.019   1.0080
>
> Thanks for your helps
>
> 05 Nisan 2011 09:03 tarihinde Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> yazdı:
>
>     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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>
>
>
> -- 
> Ahmet YILDIRIM

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