E-CAM velocities_resolve_EVC_for_LAMMPS module¶
The velocities_resolve_EVC_for_LAMMPS is a module that resolve the excluded volume constraint with a velocity formulation (no potential applied between two bonds). It is an implementation for LAMMPS of an already existing module velocities_resolve_EVC GitLab repository. The velocities_resolve_EVC_for_LAMMPS uses the module minDist2segments_KKT_for_SRP (you can find on the minDist2segments_KKT_for_SRP GitLab repository) to find the minimal distance between two bonds.
To study the long term memory of the initial conformation of a highly entangled polymer we need to preserve the topology. It means that two bonds cannot cross. It is of great importance for the study of post-mitotic chromosome unfolding. Preservation of topology is also used in the framework of Dissipative-Particle-Dynamics in particular for the study of rheological properties. To resolve the excluded volume constraints one could use a soft or hard potential between the two points (each point belong to one of the two overlapping bonds) associated to the minimal distance. Here, we propose to change the relative velocity between overlapped bonds to resolve the excluded volume constraint in one time-step of molecular dynamics. We propose to implement this functionality as a new fix for LAMMPS.
- It is used in a scientific collaboration.
- Publications: not currently available.
The present module uses the E-CAM module minDist2segments_KKT_for_SRP you can find on the minDist2segments_KKT GitLab repository. It also uses the E-CAM module velocities_resolve_EVC you can find on the velocities_resolve_EVC GitLab repository. This module is a part of a E-CAM post-doc pilot project.
You can find a pdf file with a detailed derivation of the velocity-based method we use to resolve the excluded volume constraint in one time-step of molecular dynamics on the velocities_resolve_EVC GitLab repository.
The instruction to build and run test are available on the GitLab repository. The purpose of the module is to resolve excluded volume constraints for polymer system. Therefore, we provide a simple LAMMPS input file of a system of C chains of N bonds each with volume interactions. In particular, we use the LAMMPS implementation of FENE bond. The algorithm we propose here checks every time-step the maximal overlap and exit if it exceeds a threshold you gave. It also compute a specific quantity to determine if two bonds cross during one time-step.