[gmx-users] RB-dihedral replacing 1-4 interactions

[chris.neale at utoronto.ca]

"Bond rotations in the carbon tails were modeled with Ryckaert-Bellemans
dihedrals and the corresponding 1,4 interactions removed" (Lindahl and Edholm,
Biophys J., 79, 426-433)

When doing a parameter substitution in this way, exactly what 1,4 interactions
should be removed? I am using the pope.itp file from Dr. Tieleman's website and
my specific question is why, when the double bond is atom 24 to atom 25, does
the [pairs] group contain 22-25 and 24-27, but there are no defined [pairs] for
21-24 or 25-28? 

The general structure around the double bond looks like this:

21 LP2
22 LP2
23 LP2
24 LH1
   ||     double bond
25 LH1
26 LP2
27 LP2
28 LP2

Below I have extracted any reference to atoms 21 to 28 from pope.itp:

[ atoms ]
   21    LP2    1   POPE     C21       7             0    14.0270 ; qtot:
   22    LP2    1   POPE     C22       8             0    14.0270 ; qtot:
   23    LP2    1   POPE     C23       9             0    14.0270 ; qtot:
   24    LH1    1   POPE     C24      10             0    13.0190 ; qtot:
   25    LH1    1   POPE     C25      11             0    13.0190 ; qtot:
   26    LP2    1   POPE     C26      12             0    14.0270 ; qtot:
   27    LP2    1   POPE     C27      13             0    14.0270 ; qtot:
   28    LP2    1   POPE     C28      14             0    14.0270 ; qtot:

[ bonds ]
   21    22     1   0.15300E+00 0.33470E+06
   22    23     1   0.15300E+00 0.33470E+06
   23    24     1   0.15300E+00 0.33470E+06
   24    25     1   0.13900E+00 0.41840E+06 ; double bond
   25    26     1   0.15300E+00 0.33470E+06
   26    27     1   0.15300E+00 0.33470E+06
   27    28     1   0.15300E+00 0.33470E+06

[ pairs ]
   22    25     1    ; pair around double bond
   24    27     1    ; pair around double bond

[ angles ]
   21    22    23     1     0.11100E+03   0.46020E+03
   22    23    24     1     0.11100E+03   0.46020E+03
   23    24    25     1     120.000       502.080  ; cis thingies
   24    25    26     1     120.000       502.080  ; cis thingies
   25    26    27     1     0.11100E+03   0.46020E+03
   26    27    28     1     0.11100E+03   0.46020E+03

[dihedrals] 
   21    22    23    24     3
   22    23    24    25     1 0.000       5.858      3
   23    24    25    26     2 0.000       167.360
   24    25    26    27     1 0.000       5.858      3
   25    26    27    28     3

Thanks for any assistance,
Chris Neale.