[gmx-users] charge groups
Justin A. Lemkul
jalemkul at vt.edu
Tue May 10 19:14:33 CEST 2011
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
>>
>
>
--
========================================
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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