Dear Lammps Users, How can I build a molecule structure data file for LAMMPS simulations? For example a complex structure of a chemical drug. which software is the best? and If I want to functionalize a structure such as graphene with amine group, Is it OK to construct separate structures and let them to be adsorbed during simulation spontaneously? If not how we can functionlize structures?
Some available tools are listed here: Pre/Post Processing Tools for use with LAMMPS
How you can apply them for your specific research is not something that can be answered in this generality. You will be best off by discussing with people that have already done the specific kinds of processing that you want to do. The only general remark that I can make is that building the geometry is usually the simplest part of the task, assigning atom types or finding a suitable force field (or parameterization for a specific force field) is usually the more challenging task. Also, in general, the process you describe is rather complex, but computer programs are simple things, so you will have to break down the process into multiple small and simple steps.
Thanks, I found some PDB files on the internet. I know Protein Data Bank that provide structural data of proteins. IS there any other website that provide PDB of non organic molecules? Although I can find find them on the internet but I like to know that if PDB file of any known structure is available or not.
Yes and no. You won’t find them in the same way as the PDB. That is because the PDB serves are very specific purpose for a limited category of compounds that a) follow a specific pattern of how they are constructed with very few variations and deviations and b) require additional heuristics (a residue template database with information about connectivity and force field atom type assignment) to convert the geometry and element information from the PDB file to a viable topology for atom-scale MD simulations.
For other compounds either there is more variety or no simple construction patterns, or they are less complex and can be constructed from simple rules with a custom program of its own.
For many small molecules, for example, you can construct a geometry simply from using the description of the chemical structure (e.g. in SMILES format). But, as I already mentioned in my previous response, the challenge is usually not the geometry, but the topology and the force field type assignments. Those may require some complex processing or manual editing.