[gmx-developers] strange results

[Dongsheng Zhang]

On Thu, 2006-09-07 at 08:55 +0200, David van der Spoel wrote:
> Dongsheng Zhang wrote:
> > Dear GMX developers,
> > 
> > I tried to use gromacs to check my code. At the end of day, I got some
> > strange results. I calculated the interaction energy between  one atom
> > in group CCT and twenty atoms (1-20) in group CNT. I made two cases. The
> > only difference is the charge group number for atom 1 in itp file. I got
> > different answers for these two cases.
> > 
> 
> charge groups can not be split over energy groups. maybe the check for 
> this is not adequate.
I am aware of it. In case 2, the energy group includes two charge groups
( 174 and 1). In case 1, the energy group includes only one charge group
(1). There is no complaint when I used grompp. Everything works fine
except it gives me different results (they are wrong). Do you think if
it might be a bug?



Thank you for your help!

> 
> > In case 1, part of  cnt.itp file is as following:
> > 
> > [ moleculetype ]
> > ; Name            nrexcl
> > cnt           3
> > 
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass
> > typeB    chargeB      massB
> >      1       CNTC      1    NTN     C1      1          0     12.011   ;
> > qtot 0
> >      2       CNTC      1    NTN     C2      1          0     12.011   ;
> > qtot 0
> > 
> > 
> > In case 2, part of  cnt.itp file is as following:
> > 
> > 
> > [ moleculetype ]
> > ; Name            nrexcl
> > cnt           3
> > 
> > [ atoms ]
> > ;   nr       type  resnr residue  atom   cgnr     charge       mass
> > typeB    chargeB      massB
> >      1       CNTC      1    NTN     C1    174          0     12.011   ;
> > qtot 0
> >      2       CNTC      1    NTN     C2      1          0     12.011   ;
> > qtot 0
> > 
> > The index file is as:
> > 
> > [ System ]
> > 1 .....8992
> > 
> > [ CNT ]
> >    1    2    3    4    5    6    7    8    9   10   11   12   13    
> >   14   15  16   17   18   19   20 
> > 
> > [ CCT ]
> > 4497 
> > 
> > The energy for case one is 0.000000, for case 2, it is -0.000684. In
> > fact, none is correct. The energy value in case 2 equals to the
> > interaction energy between atom 1 in CNT reacting and atom 4497 in CCT.
> > My question is why the charge group number changes the calculation
> > result. 
> > 
> > I have prepared all files. If you think it might be a bug, I can submit
> > all files. The result is reproducible.
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>