> 1. Conduct MD simulations for 100 ns for the three molecules and compare
> them with reference drugs. Without this, the study cannot be accepted.
> 2. Perform Principal Component Analysis (PCA) at different temperatures.
Adding to what Carlos said. Yes, more details, but... Practice today is
perform multiple independent simulations (different temperature random
seed, or different ion placement, or different starting configurations) to
show reproducibility in interpreted results.
https://pubs.acs.org/doi/10.1021/acs.jctc.8b00391https://pubs.acs.org/doi/10.1021/acs.jctc.8b00391
I agree with the reviewer, more sims with your molecules and the reference.
I do not see the need for PCA at different temperatures, in general, but
you did provide the context... e-mail me off the amber list if you want
help.
--tom (tec3.utah.edu)
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Received on Thu Aug 01 2024 - 23:30:02 PDT
