Dear sir,
Thank you for the detailed response. It was very insightful and helped me
get a better understanding on the reason behind choosing all atom
forcefields for protein-ligand simulations.
I have a follow up question on the same lines..
I wanted to know your opinion on the need to carry out protein-ligand MD
simulations in triplicates. From the literature, I could gather that
running Monte Carlo simulations in triplicates will make more sense, as it
is stochastic. In my humble opinion the classical MD simulations are fairly
deterministic and also as you had clearly pointed out, Protein-ligand
simulations are run for shorter durations during which, the probability of
the complex moving towards the nearest stable configuration on the free
energy landscape is quiet high. In other words, the complex gets more or
less stuck in a minima.
Do you feel this explanation could justify running the MD simulations as a
single run?
Thank you,
Regards,
Prasanth G.
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Received on Fri Mar 26 2021 - 17:30:02 PDT
