Hi,
I am in beginner level to to know about MD simulation with LAMMPS. I started with some fundamental metals and liquid (for example, copper, water and CO2) to get adapted with learning simulation. For those simulation, I got the data files from this forum and other’s research works. But, now I want to create data files for my own research work. That’s would be surfactant effects on viscosity and IFT calculation of water-surfactant solution in rock interfaces. But, I know it’s little bit hard to the define simulation box, configuration data, bond coefficient, angle coefficient and other parameters manually. Because, those have near to 10-12 atom types in together. So, I want to know, is there any particular software or way to create data files which have all of the above mentioned coefficients and parameters? Thank you.
Akash Talapatra,
Virginia Tech
Graduate Research Student
To construct a bond topology is a process that can be automated, if the choice of force field is known. There are some tools for that listed on the LAMMPS home page under pre/post processing tools. There are likely others that we don’t know about, and it is fairly straightforward to write a custom tool in python or other script languages.
The assignment of atom types (there are many more than elements as they also consider the environment of atoms) is rather tricky in comparison and finding suitable coefficients even more so. There are few tools and most are only for biomolecules, since those are based on databases with groups of atoms. So finding parameters from the published literature is hard and automating their use even harder. There is no simple way out, since this is a hard problem (if it wasn’t someone would have already done it).
Thank you for your suggestion!