Dear all,
We are working on a DNA-ligand complex. Experimentally, the ligand unwinds
the DNA. We are planning to do SMD simulations on DNA alone and DNA-ligand
complexes with the RMSD as the CV to understand the mechanism better. But
while trying to learn more about how to carry out the same, we got to know
about both SMD and ASMD. I have some very trivial questions-
1. How could one make a choice between SMD and ASMD?
2. How many replicas do we need to run in general?
THere is a tutorial for ASMD but not for SMD. COuld someone suggest some
articles which could help us understand AMBER SMD better?
THank you in advance.
Regards,
Sruthi Sudhakar
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Received on Thu May 23 2024 - 02:30:02 PDT
