[gmx-users] non-bonded [exclusions] / [ pairs ] for 56A_CARBO implementation

Jon Kapla jon.kapla at mmk.su.se
Tue Jan 17 16:42:15 CET 2012


I'm still a bit confused about the [ pairs ] and [ exclusions ] sections 
of an .itp file. How would the procedure be if I want to change the 
Lennard-Jones parameters for certain pairs of atoms in a molecule? The 
reason I ask is that I have created a trehalose topology based on the 
56A_CARBO (Hansen & Hünenberger, 2011) parameters, but I'm a bit unsure 
that I got the special 1-5 and and 1-4 pair right. This is how I did it 
(the modified forcefield is G53A6 or G54A7):

1. Excluded the pairs by putting them in the [ exclusions ] section
2. Added the excluded pairs in the [ pairs ] section with function type 
1 followed by the C6 and C12 parameters.

Something like this:

[ exclusions ]
1    5
[ pairs ]
;            ft           C6                    C12
1    5     1   0.22617E-02    0.74158E-06

Is the choice of function right? In the manual it looks like I could 
also use function type 3 here. What is more correct?

Jon Kapla


Jon Kapla
   Division of Physical Chemistry
   Dpt. of Materials and Environmental Chemistry (MMK)
   Arrhenius Laboratory
   Stockholm University
   SE-106 91 Stockholm
Pos:    PhD Student
Phone:  +46 8 16 11 79 (office)
Phone:  +46 70 304 19 89 (cell)
E-mail: jon.kapla at mmk.su.se

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