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

[ahmet yıldırım]

Dear Mark,

Now, are the files correct?
*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> 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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