Could I know any softwares which could be used credibly to go forward with protein protein interaction studies in the form of performing molecular dynamics simulation studies?
A number of softwares are available for windows:
1. Tinker for windows https://dasher.wustl.edu/tinker/
2. DIscovery studio
....
Personally, I recommend tinker .
As mentioned earlier GROMACS is an open source and very efficient for protein-protein interaction studies. You could run a simulation through a GROMACS plugin in Pymol shown as below:
https://pymolwiki.org/index.php/GROMACS_Plugin
https://bioexcel.eu/run-gromacs-within-pymol-with-dynamics/
Article Improvements in GROMACS plugin for PyMOL including implicit ...
In addition, windows 10 has inbuilt integration of ubuntu through their store. It is very easy to install just by clicks and then you can install GROMACS using sudo apt-get install gromacs. With this ubuntu, you could explore whole lot of stuff.
Hope that helps you to get going.
I suggest you Gromacs for MD simulation. It is fast and free to use.
QwikMD is a plugin of VMD and NAMD. You can install all of them on Windows (Actually, you just need to install VMD and NAMD. QwikMD comes with the most recent version of VMD). QwikMD helps you to set up an MD simulation through a graphical user interface provided by VMD.
Another suggestion would be to use desmond (md engine) via Maestro interface.
- Badges
- Science topic