I want to implement a specific algorithm for an MD or Monte Carlo Simulation of large molecules. However, I am not familiar with how molecular topology is preserved in packages like AMBER etc. I have written MD/MC codes for interacting single particles, but I am not sure how to write such code for large molecules so that to preserve bonds and chirality during the simulation.
I just want to test my algorithm so I am not considering parallelization problems as of now!
Thank you.
If you need us to help you develop your code, you have to share your code here to understand your problems in detail. Which language have you used to develop?
What do you mean by
"I have written MD/MC codes for interacting single particles, but I am not sure how to write such code for large molecules"
When you say single particles, I understand that you represented two types of forces only: electrostatic (Coulomb's for long range) and/or Van der Waals (Linard-Jones for short range). These are considered non-bonded. To add bonded forces, it will depend on how big is your molecule. for two bonded atoms you need new parameters and forces to represent bond stretching/length. for three atoms you need parameters for bond angles, and for four atoms you need parameters torsions and/or planarity (improper planes). Most softwares ignore the bonded forces beyond four atoms. Due to variations in electronic structures people use different atom "types" and some even ignore existence of non-polar hydrogen (i.e. unified atom force fields). You can find most details in molecular mechanics books.
Article Molecular Mechanics
Molecular dynamics method depends on Newton's second law and motion equations, so the force can collect from potential energy equation and acceleration from motion equations and after will make code depending on time periods to complete loop of code till reaching condition
- Badges
- Science topic