I apologize in advance if this is rudimentary...
I'm looking a protein-peptide binding interaction 87 residues - and 19
residues (complex 106).
Using the well written tutorials and literature I believe i followed the
steps correctly. (minimization, heating, acquiring an equilibrium state)
Then I did the "production" run (10 - 5ns simulations, snapshots every 5
picoseconds) I believe that I now have 50ns of simulation with 5000 frames.
Questions:
1: - are 5000 frames too many?
2: - a sodium atom was added (via addionsrand) to neutralize the system.
Would I be correct in assuming that I don't need to worry about that?
(it's not in the receptor or ligand file, only the solvated file)
Thanks,
Jonathan
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Received on Mon Dec 03 2012 - 12:30:03 PST
