E-CAM velocities_resolve_EVC module¶
velocities_resolve_EVC is a module that resolves the excluded volume constraint with a velocity formulation (no potential
applied between two overlapped bonds).
velocities_resolve_EVC uses the module E-CAM minDist2segments_KKT module to find the minimal distance between two bonds.
Purpose of Module¶
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. To resolve the excluded volume constraints you could use a soft or hard potential between the two points 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.
- Polymer simulation.
- To resolve the excluded volume constraints.
- It is used in a scientific collaboration.
- Publications: not currently available.
Note
We would use the present module to avoid topology violation in an entangled polymer system. The present module uses the E-CAM module E-CAM minDist2segments_KKT module.
Note
This module is a part of a pilot project (E-CAM post-doc). We would use it to avoid topology violation in an entangled polymer system.
Background Information¶
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.
Building and Testing¶
I provide a simple Makefile you can find at the same location as the source code.
You need C++11 in order to use pseudo-random number generator.
Before the compilation you can clean the previous build with “make mrproper” command.
The purpose of the module is to resolve excluded volume constraints.
Therefore, we provide a simple example of a system of N bonds with volume interactions.
We test every n iterations the average overlap pairwise.
Source Code¶
The source code and more information can be find at velocities_resolve_EVC GitLab repository.