Please, I sincerely (and urgently) need a suggestion on any reliable free Online tool for Molecular Dynamics (MD) Simulation. I need it to generate RMSD plot for a protein-ligand binding study I'm carrying out. Thank you in advance for your kind suggestions.
Have you tried gromacs?
https://www.gromacs.org/About_Gromacs
If you run the simulation, then you can calculate rmsd, rg, etc, by the trajectory files.
Also, see this page of Justin Lemkul:
http://www.mdtutorials.com/gmx/
I think Francisco J. Enguita will be able to help here.
Best,
Maryam
See CHARMM-GUI:
CHARMM-GUI is a web-based platform to build inputs of well-established biomolecular simulations packages. It not performs MD, but could help you with some steps:
https://www.charmm-gui.org/
I deeply appreciate your prompt suggestions so far. Many thanks. Additional suggestions are, however, also welcome.
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