[gmx-users] charge groups

[Justin A. Lemkul]

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
> 
> 

-- 
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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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