Topology violation (tv) is a post-analysis tool for computing the number of polymer chain crossing events (topology violation in polymeric system) during multi-scale simulation. In other words, tv can be equipped with molecular dynamics (MD) software such as Gromacs and LAMMPS.
Coarse-grained (CG) modelling is one of the meso-scale simulation technique that widely used in computational chemistry and biology. A concept of CG is reduction of the degree of freedom in simulated system by replacing atoms in molecule by a chunk called bead. CG modelling yeilds the resolution of simulation at larger time and scale. More details of CG modelling can be found at (https://en.wikipedia.org/wiki/Coarse-grained_modeling). This model is a promising technique that many computational chemists has waited. It can be said that CG is faster than a classical MD simulation, and still provides the accurate and reasonable results compared to experiments.
Topology violation is the event that occurs during coarse-grained simulation of soft matter such as polymer. One can determine topology violation by counting the number of chain crossing between polymer. The topology violation is a primary parameter for evaluating the coarse-grained simulation technique such as Dissipative Particle Dynamics (DPD). There are many researches using CG/DPD simulation for modelling the polymer composite based on bead-bead spring interaction instead of atomistic model.
Simulating the polymer to be consistent with the real physical properties of polymer is very important. One of the problematic issues is topology violation, which generally uccurs during the simulation. Goujon et al. studied topology violation and developed a technique to alleviate polymer chain crossing. Sirk et al. reported the modified Segmental Repulsive Potential (mSRP) in combination with DPD simulation (DPD/mSRP). Ketkaew and Tantirungrotechai made use of DPD and DPD/mSRP techniques to study the entanglement of polyisoprene (natural rubber). More practical details of DPD simulation and mSRP technique provided in LAMMPS manual.
remove_nLine bash script can be used to create a suitable XYZ coordinate file for the tv script. It will create a file named step#.txt from the raw output or trajectory file that is generated by MD software. You can find an example of XYZ coordinate in test files.
- /utility/remove_nLine
sh remove_nLine.sh
tv_script.sh can be used to run tv.py and save the analysis output. This script can help you manage tv_counting calculation when you have a ton of XYZ coordinate input files.
- /utility/tv_script.sh
sh tv_script.sh
- 2016 Thailand Computational Chemistry Challenge by UBE.
- https://sites.google.com/site/compchem403/event-news/compchem403-ceremony-tccc-ube-paccon2016
- Rangsiman Ketkaew - rangsiman1993@gmail.com