Particle-based Molecular Dynamics

All atom simulations

For now we defer to extensive guides provided elsewhere. However, the key features that one needs to be familiar with include:

1. Creating force fields and partial charges. This can either be done with a software package like AmberTools, downloaded from papers that provide force fields, or obtained from force field repositories like OpenKim or the Open Force Field Initiative.
2. Create Initial Configurations. This can be done, e.g. with tools like packmol. Standard simulation tools like AmberTools often have utility functions that aid in this process as well.
3. Create a system topology. In essence, this is an enumeration of bead type names and bonding topologies for each molecule type of interest. This can be done through manual curation with tools like Avogadro or through full stack tools like AmberTools.
4. Run. With the above data in a suitable format, one can use any all atom simulation package of preference, such as OpenMM or Gromacs. Tools like ParmEd and MoSDeF can help with conversion between file formats.

Coarse-grained simulations

We provide standard tools for rapidly setting up coarse-grained simulations using the mdfts software package and format for defining force fields and topologies.