[gmx-users] A problem? Attn: authors/developers

[David van der Spoel]

On Thu, 2004-11-18 at 19:36 -0500, Pradip Kumar Biswas wrote:
> # To whom it may concern #
> 
> While checking the individual pair of coulomb interactions for the case 
> of a water-dimer   (OA=0; HA1=1; HA2=2;  OB=3; HB1=4; HB2=5) with OPLS 
> force field in gromacs-3.2.1, I found:
> 
> For Coulomb interactions evaluated inside inl1000()  it is calculating 
> only the terms
> (verified from printing the iinr[] and jjnr[] lists & also running in 
> the gdb mode):
> 
> (v_04 + v_05) + (v_14 + v_15) + (v_24 + v_25)
> 
> Considering that due to bonds the program will not calculate the 
> coulomb for (v_01, v_02, v_12) & (v_34, v_35, v_45), the terms: v_03, 
> v_13, & v_23 which are the coulomb  interactions  with the 2nd oxygen 
> (atom_id=3) are missing from the calculation at this stage: list jjnr[] 
> contains atoms 4 & 5; atom-3 is somehow excluded!!
these are calculated in  another inner loop.
> 
> Can anybody please tell why it is so or where I am making the mistake? 
> I am new in this business; so I apologize in advance if I am drawing 
> your attention for any silly mistake.
> The residue type is taken as:
> 
> [ TIP3 ]
>   [ atoms ]
>     OH2          opls_111	-0.834  1
>      H1	   opls_112 	 0.417  1
>      H2	   opls_112 	 0.417  1
>   [ bonds ]
>     OH2   H1
>     OH2   H2
> 
> 
> Thanks in advance.
> Pradip,
> CSU, Ohio.
> 
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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://xray.bmc.uu.se/~spoel
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