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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