How to perform MD simulation on boron nitride nanosheet on GROMACS using charmm force field

User discussions
, ,
1

GROMACS version:2023.1
GROMACS modification:No
I am reaching out to seek guidance and assistance regarding a challenge I’ve encountered while attempting to simulate boron nitride nanosheets using the CHARMM force field, specifically CHARMM36. I have followed a tutorial that successfully guided me through simulating graphene; however, when attempting the same process for boron nitride, I encountered an error that stated: “CANNOT FIND FORCE FIELD FOR X ATOMS WITH X BONDS.”

I have attempted various approaches to overcome this issue, and I would like to outline the steps I have taken so far:

I generated the initial boron nitride nanosheet structures using GaussView and saved them in PDB format.

I used VMD (Visual Molecular Dynamics) to convert the PDB-formatted structures into GRO format, following the procedure outlined in the tutorial.

I attempted to use the editconf tool to prepare the simulation box and system for further processing.

I defined a .n2t file to specify atom types for boron and nitrogen atoms.

I extended the .atp file to incorporate the newly defined atom types.

I updated the bonded and nonbonded parameter files (.itp) to include relevant parameters for boron nitride atoms.(I obtained the parameters from literature but it would be great help if someone could also recommend the force constants that could be used.I am attaching the n2t file along with the gro files.

If anyone has successfully simulated boron nitride nanosheet or has expertise in this area, I would greatly appreciate your guidance and insights. Specifically, I am looking for a reliable method to simulate boron nitride nanosheets.I think the problem is either in the gro files that I have created using editconf command following this tutorial(Modeling Carbon Nanotubes with GROMACS - Chembytes ) or I am unable to define the atom types correctly.

#boronnitride #MD simulation #CHARMM #GROMACS

2

hi! the problem was solved the issue was in the format of pdb that I was getting from guassview along with n2t file I had set the distances in different unit(angstorm rather than nanometer)

3

Mam can you please share your n2t files and .itp files. As iam trying to do a simulation involving boron nitride. Mam it would be of great help if you please share the files . As mam when I ran the simulation, it showed scattered atoms of boron and nitrogen all over , this happened because I didn’t specify bonds in the residue file of gromos53a6 forcefield. For specific bond, dihedrals and impropers, I need a proper itp file for boron nitride , which iam not able to find anywhere. Please help 🙏