[gmx-users] A problem? Attn: authors/developers
Pradip Kumar Biswas
p.biswas at csuohio.edu
Fri Nov 19 01:36:46 CET 2004
# 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!!
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 ]
Thanks in advance.
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