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 (http://chembytes.wikidot.com/grocnt#toc) 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.
#boronnitride #MD simulation #CHARMM #GROMACS
Unfortunately the only boron parameters you will find in CHARMM is for boronic acids (BO4), which means that you only have parameters for B - C and B - O, not B - N.
You will have to generate these parameters by QM (bonds and angles) using the equations available in the GROMACS manual to obtain the corresponding bond lengths/force and angle/force.
The file that you have is only half the solution (you can see bond lengths but thats all).
If you have access to CHARMM-GUI you can try to get the missing parameters from it (and then convert them to GROMACS format).
Dear Ricardo J Ferreira thank you for your time.I obtained the parameter for boron nitride from literature and included them in nonbondedff.itp and with a few changes in n2t file, I was able to obtain the topology file. But the problem I am encountering now is the following ERROR "Trying to add Buck.ham (SR) while the default nonbonded type is LJ" occurs when I try to add ions to the system. I checked all the itp files to make sure that type field is set to 1 in the [ nonbond_params ] section.Given your profound expertise and experience in this field, I would greatly appreciate any guidance you could provide on this matter.
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