[gmx-users] charge groups

[Gavin Melaugh]

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}


Justin A. Lemkul wrote:
>
>
> Gavin Melaugh wrote:
>> Hi Justin
>>
>> The two files processed.top and topol.top are the exact same. What is
>> worrying me is that when I look at the topol.tpr from gmxdump, my charge
>> groups do not seem to be specified the way I stated in the topology
>> file.
>>
>
> Can you provide a relevant snippet of the gmxdump output to
> demonstrate this?
>
> Consecutive numbering is not stated as a requirement in the manual,
> and if it is in the code, then it needs to be either documented as
> being necessary, and/or an enhancement request needs to be filed on
> redmine for non-consecutive charge group numbering.
>
> -Justin
>
>> Gavin
>>
>> Justin A. Lemkul wrote:
>>>
>>> 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
>>
>>
>