Topology file error

User discussions
1

GROMACS version: 2024.1-Homebrew
GROMACS modification: No
Here post your question: Hi, I am a new user trying to simulate 2 LJ spheres but am having trouble with the topology file. I am getting the error “Molecule type ‘LJ1’ contains no atoms”

Gro file (had trouble formatting it; ended up using openmm to make a pdb then converting it to a gro file with gmx editconf):
LJ Spheres
2
1LJ LJ1 1 0.100 0.000 0.000
2LJ LJ2 2 0.400 0.000 0.000
3.00000 3.00000 3.00000

Top file currently:
; Lennard-Jones spheres topology

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0

[ atomtypes ]
; name mass charge ptype sigma epsilon
LJ1 1.0 0.0 A 0.34 0.996
LJ2 1.0 0.0 A 0.34 0.996

[ moleculetype ]
; name nrexcl
LJ1 1
LJ2 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 LJ1 1 LJ1 LJ1 1 0.0 1.0
2 LJ2 2 LJ2 LJ2 1 0.0 1.0

[ system ]
; Name
Lennard-Jones Spheres

[ molecules ]
; Compound nmols
LJ1 1
LJ2 1

I have also tried separating the sections for each particle type:
; Lennard-Jones spheres topology

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0

[ atomtypes ]
; name mass charge ptype sigma epsilon
LJ1 1.0 0.0 A 0.34 0.996

[ moleculetype ]
; name nrexcl
LJ1 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 LJ1 1 LJ1 LJ1 1 0.0 1.0

[ atomtypes ]
; name mass charge ptype sigma epsilon
LJ2 1.0 0.0 A 0.34 0.996

[ moleculetype ]
; name nrexcl
LJ1 1
LJ2 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
2 LJ2 2 LJ2 LJ2 1 0.0 1.0

[ system ]
; Name
Lennard-Jones Spheres

[ molecules ]
; Compound nmols
LJ1 1
LJ2 1

But get ‘invalid order for directive atomtypes’ error

2

All atom types must be defined before any atoms (like in your first example). Molecule types must be defined separately and one at a time.
Try

; Lennard-Jones spheres topology

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0

[ atomtypes ]
; name mass charge ptype sigma epsilon
LJ1 1.0 0.0 A 0.34 0.996
LJ2 1.0 0.0 A 0.34 0.996

[ moleculetype ]
; name nrexcl
LJ1 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 LJ1 1 LJ1 LJ1 1 0.0 1.0

[ moleculetype ]
; name nrexcl
LJ2 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 LJ2 1 LJ2 LJ2 1 0.0 1.0

[ system ]
; Name
Lennard-Jones Spheres

[ molecules ]
; Compound nmols
LJ1 1
LJ2 1

or you can manage with one atom type:

; Lennard-Jones spheres topology

[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 1 no 1.0 1.0

[ atomtypes ]
; name mass charge ptype sigma epsilon
LJ 1.0 0.0 A 0.34 0.996

[ moleculetype ]
; name nrexcl
LJ1 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 LJ 1 LJ1 LJ1 1 0.0 1.0

[ moleculetype ]
; name nrexcl
LJ2 1

[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 LJ 1 LJ2 LJ2 1 0.0 1.0

[ system ]
; Name
Lennard-Jones Spheres

[ molecules ]
; Compound nmols
LJ1 1
LJ2 1
3

Thank you!