Dear all,
We are working on a DNA-ligand complex. Experimentally, the ligand unwinds
the DNA. We carried out SMD simulations on DNA alone and DNA-ligand
complexes. However, I have a few queries:
1. When we do asmd as per the amber tutorial we finally get a pmf plot, how
to plot/calculate work from this?
2. If I have done 1ns/angstroms simulation with 50 TPS in 5 stages, should
I consider just the one minima on the final PMF plot for interpretation?
Any suggestions will be appreciated.
Regards,
Sruthi Sudhakar
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Received on Tue Jul 02 2024 - 02:30:02 PDT
