Running atomistic simulations in GROMACS

User discussions
1

GROMACS version: 2020.5
GROMACS modification: No

Hello. I am new to GROMACS and I have done some of the tutorials on GROMACS Tutorials.

I am trying to recreate results in the paper * Soft Matter, 2017, 13, 1904* for atomistic benzene. In this paper, they perform simulations with benzene modeled using the CHARMM forcefield.
This is how I am proceeding with it is:

  1. I created a benzene ring in Avogadro
  2. Obtained a .pdb file from the benzene structure.
    My benzene pdb file was:
    COMPND UNNAMED
    AUTHOR GENERATED BY OPEN BABEL 2.3.90
    HETATM 1 C UNL 1 0.494 -1.549 1.068 1.00 0.00 C
    HETATM 2 C UNL 1 -0.848 -1.905 1.196 1.00 0.00 C
    HETATM 3 C UNL 1 -1.778 -0.969 1.649 1.00 0.00 C
    HETATM 4 C UNL 1 -1.366 0.323 1.973 1.00 0.00 C
    HETATM 5 C UNL 1 -0.023 0.680 1.844 1.00 0.00 C
    HETATM 6 C UNL 1 0.906 -0.256 1.392 1.00 0.00 C
    HETATM 7 H UNL 1 1.219 -2.278 0.716 1.00 0.00 H
    HETATM 8 H UNL 1 -1.170 -2.912 0.944 1.00 0.00 H
    HETATM 9 H UNL 1 -2.824 -1.247 1.749 1.00 0.00 H
    HETATM 10 H UNL 1 -2.090 1.053 2.325 1.00 0.00 H
    HETATM 11 H UNL 1 0.298 1.687 2.096 1.00 0.00 H
    HETATM 12 H UNL 1 1.952 0.022 1.292 1.00 0.00 H
    CONECT 1 2 6 7
    CONECT 2 1 3 8
    CONECT 3 2 4 9
    CONECT 4 3 5 10
    CONECT 5 4 6 11
    CONECT 6 1 5 12
    CONECT 7 1
    CONECT 8 2
    CONECT 9 3
    CONECT 10 4
    CONECT 11 5
    CONECT 12 6
    MASTER 0 0 0 0 0 0 0 0 12 0 12 0
    END
  3. then i ran gmx pdb2gmx -f c6h6.pdb -o c6h6.gro
  4. Selecting CHARMM forcefield when the prompt pops up (Option 8)
  5. Selecting SPC model for water (no particular reason)
  6. I got this error message:
    Fatal error:
    Residue ‘UNL’ not found in residue topology database

I understand that UNL is not a classical amino acid residue, but I am wondering how to enter atomistic representations in GROMACS, that don’t come from the Protein Databank.

On a tangential note, if I had to model water (even though I know GROMACS has SPC(E)/TIPxP models in-built, could I enter a model for water I made and let GROMACS run it? How would I do such a thing? I know this is possible in LAMMPS, but I am unsure about how to do this in GROMACS.

2

Hi,

I understand that UNL is not a classical amino acid residue, but I am wondering how to enter atomistic representations in GROMACS, that don’t come from the Protein Databank.

To be recognized by pdb2gmx your molecular should be defined in the force field database file (*rtp). Here you see more on the force field structure in GROMACS.
https://manual.gromacs.org/current/reference-manual/topologies/pdb2gmx-input-files.html#pdb2gmxfiles

There are also webserver that can generate small molecules topology

On a tangential note, if I had to model water (even though I know GROMACS has SPC(E)/TIPxP models in-built, could I enter a model for water I made and let GROMACS run it? How would I do such a thing? I know this is possible in LAMMPS, but I am unsure about how to do this in GROMACS.

Yes you can implement your water molecule and other molecule models in GROMACS. Here some links on the topology structure.

https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html?highlight=force%20field%20table

https://manual.gromacs.org/current/reference-manual/topologies/parameter-files.html

https://manual.gromacs.org/current/how-to/topology.html?highlight=atom%20type

I hope it helps
Best regards
Alessandra