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Here post your question : Iam trying to simulate boron nitride through a lipid membrane. I made the system and the topology and the system was well equilibriated. After I ran the final md production, I loaded the trajectory file in vmd and the system was showing some weird line structure, distorted instead of an actual lipid bilayer and boron nitride. I tried using trjconv function to fix this . First I centered the system by selecting system that consisted of 19650 atoms as input and same system as output . Then I ran the trjconv with the recentered file. This gave a start pdb which consisted a snapshot of my simulation. After loading to visualise it I saw the lipid bilayer broken from one side and the boron nitride not to be seen anywhere. What could be the issue and should I fix this . Can anyone please help me as soon as possible as I have a competition to participate day after tomorrow. Pls help
Please have a look at the User guide: https://manual.gromacs.org/current/user-guide/terminology.html#gmx-pbc. Hopefully that will help you.
Thank you very much sir for the prompt reply , I will try this out and will update you
Sir I got a snapshot of one of the frames by applying gmx trjconv function . Iam attaching the screenshot of the same here . The lipid layer is somewhat intact however I can see some of the molecules broken . The boron nitride sheet is totally broken and you can see blue and yellow dots . Those are broken nitrogen and boron atoms . I applied the -pbc whole function but the boron nitride layer was still not recovering. How can I fix this . I want the sheet to be intact .
If the molecules are not whole after using the -pbc whole option then I would assume that the molecules are not correctly constructed in the topology, i.e., not defined as molecules. You might also want to make sure that all bonds are present in the coordinate file you use as topology when opening the trajectory in VMD. If the bonds are not defined, or slightly too long, VMD might not recognise them as bonds. In that case, you can try using the graphical representation option DynamicBonds and
increase the distance cutoff in VMD.
If you would just like to place the atoms inside the periodic box, you can use the -pbc mol option on the trajectory you got when having applied -pbc whole.
Sir in understood the issue, maybe it seems that while extending the gromos53a6 forcefield for boron nitride, I just gave the parameters for atoms . I didn’t give parameters related to bonds . Sir can that can be an issue .
Yes, if you have not specified that the atoms are connected by bonds, and specified the bond parameters, they will be completely disconnected.
Sir , actually the issue is that boron nitride is not defined in any of the forcefields available in gromacs . Also I would require a full fledged. .itp file for all the parameters. There is no website that can make a topology file i.e a .itp file for boron nitride. I tried many websites , but they gave errors . The parameters I had fed initially building the system were just the epsilon and the sigma value for boron and nitrogen. These values I have obtained by referring research articles. So sir where can I get dihedrals, bonds , pairs from for boron nitride.
Sir I also tried the nanotube / nanosheet builder plugin available in vmd . But sir it only allows me to load the coordinates in pdb format and not in itp format
Yes, you need a full .itp file for all the parameters. That can be a challenge when simulating complex molecules. If you break your molecule down to a representative building block it is possible that you can get a reasonable estimate of bond, angle and dihedral parameters from https://charmm-gui.org, GitHub - alanwilter/acpype: OFFICIAL: AnteChamber PYthon Parser interfacE or GROMACS / STaGE · GitLab (requiring many external tools). But you will almost certainly have to make a script to then generate the full parameter set for your polymer.
Sir i fed all bonded parameters now , but still it is showing single atoms and now the system fails at the nvt step saying water cannot be settled. What should I do sir
One more thing that I noticed is that when I give the gmx pdb2gmx command to make the topology then , the topology section for boron nitride sheet does not have any bonds specified in the topol.top. I even tried adding the bonds and dihedrals section manually in the topol.top file so that the grommp comand can read that , but got no luck.