[gmx-users] charge groups

[Gavin Melaugh]

Also. Obviously I arranged the charge groups like this so that they
would be neutral, I just didn't realise that the atoms comprising the
charge groups had to be in sequence.

Justin A. Lemkul wrote:
>
>
> 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
>