[gmx-users] charge groups

[Gavin Melaugh]

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.

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
>