[gmx-users] charge groups

[Justin A. Lemkul]

Gavin Melaugh wrote:
> O.K cheers
> I assume that this is irrelevant in vacuum with no cut-offs
> 

Or (for reference) with PME, I would suspect, since in this case charge groups 
do not have to be net neutral.

-Justin

> Gavin
> 
> 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
>>
> 
> 

-- 
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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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