[gmx-users] Questions about the topology file format

[Ebert Maximilian]

Hi there,

I have two quick questions about the topology file format which I couldn’t find in the documentary. The semi-colon is giving me some headache. Is it always a comment which is written after?

First:

[ atoms ]
;   nr  type  resi  res  atom  cgnr     charge      mass       ; qtot   bond_type
     1 opls_135     1   IPA    C1    1    -0.111600     12.01100 ; qtot -0.112  CT 

is qtot and CT used for anything and is it interpreted since it is after the ;

Second:

[ bonds ]
;   ai     aj funct   r             k
     1      2   1 ;    1.5350e-01    2.5363e+05 ;     C1 - C2         CT - CT    

are the values for r and k here used since they are after the ; and what is C1-C2 and CT-CT used for and why another ;?

Thank you very much for clarification.

Max