[gmx-users] Trouble running simulations with Nitrogen

Joshua Cummings Joshua.Cummings at uon.edu.au
Fri Jul 20 05:55:05 CEST 2018

Hi Everyone,

I'm currently trying to run some simulations that involve the absorption of N2 into a liquid solvent. I'm having some difficulty in generating the topology for N2. For reference, the pdb file I have for N2 is as follows:

HETATM    1  N6B HDZ     0       0.000   0.000   0.553  1.00  0.00           N
HETATM    2  N6A HDZ     0       0.000   0.000  -0.553  1.00  0.00           N
CONECT    1    2
CONECT    2    1

When I try to generate the .itp file and topology via pdb2gmx (OPLS), gromacs doesn't recognise the residue. I've tried using both the LigParGen server and the PRODRG to generate the topology, but neither work. PRODRG generates an error saying it does not deal with mono/di-atomic molecules and LigParGen won't recognise N2 at all.

I haven't had any trouble generating topologies for other small gas molecules such as CH4, am I missing something here or are OPLS parameters not possible for N2? Should I use some other forcefield for N2?

Thanks in advance everyone,

JOSHUA Cummings

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