[gmx-users] Interpreting dihedrals in topology file

[rdwducl]

Hello.

Below is an extract from a topology file (it describes the CTAC surfactant).

I am trying to convert this into a DL_POLY FIELD file (I am not a GROMACS
user) but am having difficulty interpreting some of it, despite reading
through the manual.

Questions:

1. Does including pairs in the [ pairs ] directive cause the non-bonding 4-1
interactions to be INCLUDED or EXCLUDED?

2. The [ pairs ] directive includes 15-18 and 15-19 pairs, but neither of
these pairs appear in any of the dihedrals together (nor in any other
interaction). So what effect does it have to include them?

Thanks very much for any guidance!


; -------- 8<
---------------------------------------------------------------------
[ pairs ]
; ai  aj  fu    c0, c1, ...
  14  17   1                                           ;    C3    N   
  15  18   1                                           ;    C2  CN1   
  15  19   1                                           ;    C2  CN2   
  15  20   1                                           ;    C2  CN3 

[ dihedrals ]
; ai  aj  ak  al  fu    c0, c1, m, ...
  17  16  19  18   2     35.3  334.8       35.3  334.8   ; imp     N   C1 
CN2  CN1    
   4   3   2   1   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C13  C14  C15  C16   
   5   4   3   2   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C12  C13  C14  C15   
   6   5   4   3   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C11  C12  C13  C14   
   7   6   5   4   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C10  C11  C12  C13   
   8   7   6   5   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C9   C10  C11  C12   
   9   8   7   6   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C8   C9   C40  C11   
  10   9   8   7   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C7   C8   C9   C40   
  11  10   9   8   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C6   C7   C8   C9   
  12  11  10   9   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C5   C6   C7   C8   
  13  12  11  10   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C4   C5   C6   C7   
  14  13  12  11   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C3   C4   C5   C6   
  15  14  13  12   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C2   C3   C4   C5   
  16  15  14  13   3      9.2789   12.156  -13.120 -3.0597 26.240 -31.495 ;
dih   C1   C2   C3   C4     
  17  16  15  14   1      0.0    5.9 3      0.0    5.9 3 ; dih     N   C1  
C2   C3   
  15  16  17  20   1      0.0    3.8 3      0.0    3.8 3 ; dih    C2   C1   
N  CN3 
; -------- 8<
---------------------------------------------------------------------





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