[gmx-users] A problem? Attn: authors/developers
David van der Spoel
spoel at xray.bmc.uu.se
Fri Nov 19 10:15:03 CET 2004
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.
> CSU, Ohio.
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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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