Molecular Modelling - Innovation Lab 2020

  Building a LAMMPS data file manually can be awfully time-consuming, especially for larger systems. In order to expedite the process, it is possible to use some widely available software to generate the initial file which contains atomic and molecular information. For instance, CHARMM-GUI ( see link ) could be a useful tool to generate LAMMPS data files for biological systems. However, we have not been able to find any free-to-use software for creating LAMMPS data files for more general applications. The most accessible option is to generate a different file with a robust molecular format, such as .mol2. This particular format seems like a great choice because it offers a vast array of stored information. Most importantly, these files could specify the XYZ coordinates of atoms, their atom symbols, hybridisation, certain connectivity types, charges, molecule IDs, and IDs of bonded atoms. To execute the initial task of generating a .mol2 file, we found that the most useful programs ...

Please download this .cpp file ; a preview isn't available.

So far the efforts into our case study resulted in a questionable simulation of an unnaturally behaving bunch of phospholipids, though it is not an issue that cannot be fixed later. To access the simulation recording, please click on the image below.

 We love hyperlinks, so here are three more leading you to yet another crucial part of our project:

Some helpful tools in running a LAMMPS simulation are described in the document found  > here < .

 > find a new tutorial here <

We've promised to explain how to get started with LAMMPS and today's tutorial on creating data files is being uploaded this evening. Good night and good luck! > Creating Data Files <