Adding hydrogen on boron nitride sheet in VMD

Rajesh, The number of angles dihedrals and impropers can be generated using topotools, moltemplate…etc. Also you have to figure out the right parameters for those angles and dihedrals, bonds, Lj coefficients, partial charges. This typically is provided by the force filed. Using the right parameters is crucial for an MD simulation.

From the way you have framed your questions I feels that you need to work on simple systems. Try generating topology and the fixing the right parameters for the small system using vmd or moltemplate. Verify your results, validate them build your confidence and then move on to BNsheet or whatever complicated system you are working.

Also try setting up small examples in lammps and familiarize yourself with what the lammps command does and their keywords.


Sir, for small system also we need to add hydrogen to the existing small system. And I dont understand how to add that. parameters can be calculated using any force field . I am stuck at initial step itself.