I need to run molecular dynamic simulation for a protein-protein complex which i obtain from HADDOCK server. Are there any web servers which i can run md simulation? If yes ,could anyone suggest me one of them which is more acurate and can use in educational publication purposes?I appreciate it if you provide me with an answer.
Thank you in advance
Dear Shamali Abeywardhana
Yes, a few are available for limited resources, but I will suggest downloading any desktop-based software and running by yourself, i.e., Gromacs, NAMD, Desmond, Amber etc.
Here are some of the servers for running short MDS:
1) CABS-Flex (biocomp.chem.uw.edu.pl/CABSflex2)
2) Simplerun (https://www.playmolecule.com/SimpleRun/)
Alternatively, you can run MDS on Google Colab. Refer to the following article:
Making it rain: cloud-based molecular simulations for everyone
(https://chemrxiv.org/engage/chemrxiv/article-details/6116a01f424ea3ed758921a7)
- Badges
- Science topic