[gmx-developers] strange results

[David van der Spoel]

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.


> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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