How would I do MM-PBSA analysis after MD simulations in GROMACS?

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Justin Lemkul Popular answer

http://rashmikumari.github.io/g_mmpbsa/

Justin Lemkul

Sidra Rafi

http://www.sciencedirect.com/science/article/pii/S0010465514003154

Mayur Mukhi

Justin Lemkul How do I know how much of the trajectory or how many frames I should use for the MM-PBSA analysis?

Fatemeh Haghighi

Check the RMSD

Fatemeh Haghighi How do I tell from the RMSD? Could you please elaborate. Thanks in advance!

You should take the period where RMSD of the protein is stable.

Fatemeh Haghighi Got it. Thank you very much!

You're welcome