Difference between bond function type 1 and 6

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GROMACS version: 2018
GROMACS modification: No
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Dear all,

I am a newbie user of GROMACS. I want to write my top file using OPLS-AA force field. For bonded interactions OPLS-AA employs this functional form

V(r) = Kb * (r-b0)^2

, where Kb is the bond constant, b0 is the interatomic equilibrium distance and r is the interatomic distance.

I was wondering which is the difference between the function type 1 (‘bond’) and 6 (‘harmonic potential’) reported in the manual for the bonded interactions. For both of them Kb has the same units.

I would be very grateful if any of you could help me.

Thank you very much in advance.

Best regards,
Emma Rossi

2

Type 6 “bonds” do not generate exclusions for 1-4 interactions; they are not true “chemical” bonds in that sense. It’s just a harmonic potential between the two atoms.

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