Structure of .top File

User discussions
1

GROMACS version: 2023.1
GROMACS modification: No

Hello

Below is my .top file with GAFF obtained from the ACPYPE server and it works well. Am I good to go or I have to include something like (“include ./gaff.ff/forcefield.itp”) as in most of such files?

; Topology of the system

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333333333

[ atomtypes ]
;name   bond_type     mass     charge   ptype   sigma         epsilon       Amb
 c3       c3          0.00000  0.00000   A     3.39967e-01   4.57730e-01 ; 1.91  0.1094
 p5       p5          0.00000  0.00000   A     3.74177e-01   8.36800e-01 ; 2.10  0.2000
 hc       hc          0.00000  0.00000   A     2.64953e-01   6.56888e-02 ; 1.49  0.0157
 c        c           0.00000  0.00000   A     3.39967e-01   3.59824e-01 ; 1.91  0.0860
 o        o           0.00000  0.00000   A     2.95992e-01   8.78640e-01 ; 1.66  0.2100

#include "tbp.itp"
#include "ace.itp"


[ system ]
 Pure Ionic Liquid

[ molecules ]
; Compound        nmols
 TBP             500
 ACE             500
2

The typically included force field sections are atomtypes (defining LJ parameters) and bonded interaction types. You’ve got your atomtypes defined here (assuming these are all you need for your molecules), and I guess your .itp files might have the bonded parameters listed explicitly in the [ bonds ], [ angles ] etc. sections. If that is indeed the case, then you don’t need anything else; either way, gmx grompp will explicitly tell you if there’s something missing in the topology.

3

Dear @milosz.wieczor

Of course my .itp files include required parameters under: [ atom ], [ bonds ], [ pairs ], [ angles ], and proper [ dihedrals ].

Thank You.