[gmx-users] charge groups

[Justin A. Lemkul]

Gavin Melaugh wrote:
> As you can see atomnr 7 HC should belong to the same charge group (1) as
> atomnr 1&2. From the tpr file atomnr 7 (in this file 6) seems to have
> its own charge group (3).
> 
> [atoms]
> ; atomnr  type   resnr  residue   name    cgnr     charge     mass
>     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        CB       2      0.0000     12.0110
>     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
>    14      CU       1   CGE        CU      15      0.2650     13.0190
>    15      NU       1   CGE        NU      15     -0.5970     14.0070
> 
>     cgs:
>          nr=112
>          cgs[0]={0..1}
>          cgs[1]={2..3}
>          cgs[2]={4..5}
>          cgs[3]={6..6}
>          cgs[4]={7..8}
>          cgs[5]={9..9}
>          cgs[6]={10..11}
>          cgs[7]={12..12}
>          cgs[8]={13..14}
>          cgs[9]={15..16}
>          cgs[10]={17..18}
>          cgs[11]={19..20}
>          cgs[12]={21..21}
>          cgs[13]={22..23}
>          cgs[14]={24..24}
>          cgs[15]={25..26}
>          cgs[16]={27..27}
>          cgs[17]={28..29}
>          cgs[18]={30..31}
>          cgs[19]={32..33}
>          cgs[20]={34..35}
>          cgs[21]={36..36}
>          cgs[22]={37..38}
>          cgs[23]={39..39}
>          cgs[24]={40..41}
>          cgs[25]={42..42}
>          cgs[26]={43..44}
>          cgs[27]={45..46}
> 
> 

Then it seems pretty clear that one cannot have discontinuous charge groups.  I 
will find somewhere to put this fact in the manual.  It may be a useful 
enhancement request.  If you need these discontinuous charge groups in your 
topology, you'll have to reorganize it such that all grouped atoms are consecutive.

-Justin

-- 
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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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