Let's look at what is in the output topology (topol.top). Again, using a plain text editor, inspect its contents. After several comment lines (preceded by ;), you will find the following:

#include "charmm36.ff/forcefield.itp"

This line calls the parameters within the CHARMM36 force field. It is at the beginning of the file, indicating that all subsequent parameters are derived from this force field. The next important line is [ moleculetype ], below which you will find

; Name            nrexcl
Protein_chain_A     3

The name "Protein_chain_A" defines the molecule name, based on the fact that the protein was labeled as chain A in the PDB file. There are 3 exclusions for bonded neighbors. More information on exclusions can be found in the GROMACS manual; a discussion of this information is beyond the scope of this tutorial.

The next section defines the [ atoms ] in the protein. The information is presented as columns:

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
; residue   1 LYS rtp LYS  q +2.0
     1        NH3      1    LYS      N      1       -0.3     14.007
     2         HC      1    LYS     H1      2       0.33      1.008
     3         HC      1    LYS     H2      3       0.33      1.008
     4         HC      1    LYS     H3      4       0.33      1.008
     5        CT1      1    LYS     CA      5       0.21     12.011
     6        HB1      1    LYS     HA      6        0.1      1.008

The interpretation of this information is as follows:

• nr: Atom number
  For each moleculetype, this numbering must start from 1 and is a running count of the number of atoms in the molecule.
• type: Atom type
  The designation of an atom type determines the Lennard-Jones parameters assigned to each atom.
• resnr: Amino acid residue number
• residue: The amino acid residue name
  Note that this residue was "LYS" in the PDB file; the use of .rtp entry "LYS" indicates that the residue is protonated using the CHARMM naming convention (the predominant state at neutral pH). In this force field, "LSN" would indicate neutral (no net charge) lysine.
• atom: Atom name
• cgnr: Charge group number
  Charge groups define units of integer charge; this is an old convention for trying to speed up calculations and are largely irrelevant these days.
• charge: The partial charge assigned to each atom.
  The "qtot" descriptor is a running total of the charge on the molecule
• mass: Self-explanatory
• typeB, chargeB, massB: Used for free energy perturbation (not discussed here)

Subsequent sections include [ bonds ], [ pairs ], [ angles ], and [ dihedrals ]. Some of these sections are self-explanatory (bonds, angles, and dihedrals). The parameters and function types associated with these sections are elaborated on in Chapter 5 of the GROMACS manual. Special 1-4 interactions are included under "pairs" (section 5.5.2 of the GROMACS PDF manual or linked here).

The remainder of the file involves defining a few other useful/necessary topologies, starting with position restraints. The "posre.itp" file was generated by pdb2gmx; it defines a force constant used to keep atoms in place during equilibration (more on this later).

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

This ends the "Protein_chain_A" moleculetype definition. The remainder of the topology file is dedicated to defining other molecules and providing system-level descriptions. The next moleculetype (by default) is the solvent, in this case TIP3P water. Other choices for water include SPC, TIP3P, and TIP4P. We chose this model by passing "-water tip3p" to pdb2gmx. For an excellent summary of the many different water models, click here, but be aware that not all of these models are present within GROMACS.

; Include water topology
#include "charmm36.ff/tip3p.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
#endif

As you can see, water can also be position-restrained, using a force constant (k_pr) of 1000 kJ mol^-1 nm^-2.

Ion parameters are included next:

; Include generic topology for ions
#include "charmm36.ff/ions.itp"

Finally come system-level definitions. The [ system ] directive gives the name of the system that will be written to output files during the simulation. The [ molecules ] directive lists all of the molecules in the system.

[ system ]
; Name
LYSOZYME

[ molecules ]
; Compound        #mols
Protein_chain_A     1

A few key notes about the [ molecules ] directive:

1. The order of the listed molecules must exactly match the order of the molecules in the coordinate (in this case, .gro) file.
2. The names listed must match the [ moleculetype ] name for each species, not residue names or anything else.

If you fail to satisfy these concrete requirements at any time, you will get fatal errors from grompp (discussed later) about mismatched names, molecules not being found, or a number of others.

Now that we have examined the contents of a topology file, we can continue building our system.