Whether periodic molecules = yes leads to visualisation of a polymer structure in simulations

User discussions
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GROMACS version:
GROMACS modification: Yes/No
Here post your question : Iam trying to simulate boron nitride sheet . Initially I didn’t define the bonds, dihedrals in residue.rtp file of gromos53a6 forcefield. After running the md run production I got a simulation where the HBn sheet could be seen as individual boron and nitrogen atoms . In the next trail , i did specify bonds and dihedrals. Then too the same issue arrived . Then i tried to define periodic- molecules= yes in mdp file of both nvt and em step . What should I do to make the sheet appear intact

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The visualization has nothing to do with what bonds you specify for GROMACS. Not seing bonds in the visualization doesn’t tell you much on whether there are present in the simulation.

I don’t see how you can define bonds for a whole sheet in the residue.rtp file. pdb2gmx can only generate topologies for linear molecules. I think you would need generate the topology manually.

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So sir , does this mean that i need to manually write each and every bond in .rtp file for the boron nitride sheet. As while specifying the bonds , i just specified two bonds . B-N and N-B and accordingly the same way I specified the dihedrals .

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Is there any way that I can render the HBn sheet intact . Or is it that the force applied is too large and that’s the reason behind the system breaking

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If you have not provided all bonds in the topology then there is nothing keeping it together.

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And as Berk said, the .rtp file is used by pdb2gmx to generate the topology. For a whole polymer sheet you can probably not use pdb2gmx. But you can probably generate the topology file yourself using a python script, or something.

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I tried using a python script developed by one of the gromacs forum member called Gentopo. But that doesn’t run and give me a topology file. What should I do sir , is there any way out .

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Have a look at topology files and read the documentation https://manual.gromacs.org/current/reference-manual/topologies/topology-file-formats.html#topology-file and https://manual.gromacs.org/current/reference-manual/topologies/parameter-files.html#parameter-files.

If you’ve already got the parameters for the required bonds, angles and dihedrals, I don’t think it should be very difficult for you to make a python script that populates the [ bonds ], [ angles ] and [ dihedrals ] sections. You may also need [ pairs ].

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Ok sir I’ll try doing this