Dear all,
I am learning to perform the Umbrella Sampling to get the PMF between two
states of a DNA strand. And I have trouble determining the reaction
coordinates. The difference between the two states is that the hydrogen
bonds they form are not the same. I think the transition is more like
rotating the base in the plane of the base ring (around the z-axis). I see
that the tutorial examples on Amber's site use reaction coordinates like
angles or distances. But I can't think of any angle that would control the
transition of the structures I have. Anyone have suggestions?
Thanks in advance,
Jing
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Received on Fri Sep 08 2023 - 14:00:02 PDT
