[gmx-users] charge groups

[Justin A. Lemkul]

Gavin Melaugh wrote:
> Hi all
> 
> Do atoms belonging to the same charge group have to be indexed
> consecutively in the topology file or can you have the following.
> 
> [atoms]
>    1       CA       1   CGE        CA       1     -0.1150     12.0110
>     2      CB       1   CGE        CB       1      0.0000     12.0110
>     3      CA       1   CGE        CA       2     -0.1150     12.0110
>     4      CB       1   CGE       :wq
>  CB       2      0.0000     12.0110

Assuming you fix this, then yes, splitting charge groups can work.  Use grompp 
-pp to see the post-processed topology to make sure everything came out as expected.

-Justin

>     5      CA       1   CGE        CA       3     -0.1150     12.0110
>     6      CB       1   CGE        CB       3      0.0000     12.0110
>     7      HC       1   CGE        HC       1      0.1150      1.0080
>     8      CU       1   CGE        CU      13      0.2650     13.0190
>     9      NU       1   CGE        NU      13     -0.5970     14.0070
>    10      HC       1   CGE        HC       2      0.1150      1.0080
>    11      CU       1   CGE        CU      14      0.2650     13.0190
>    12      NU       1   CGE        NU      14     -0.5970     14.0070
>    13      HC       1   CGE        HC       3      0.1150      1.0080
> 
> Cheers
> 
> Gavin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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