Hello Amber users,
I'm going to calculate free energy using umbrella sampling and have trouble with reaction coordinate definition in the .rst file.
Before calculating free energy, I applied PCA to the initial trajectory and find a initial path in the first five modes space using certain method. So I want to use the same reaction coordinates, or CVs, in free energy calculation. That's to say define the reaction coordinate of a frame as its projection values to the given five modes(or PCs). How can I do this? Are there some user-defined way in Amber umbrella sampling?
Thank you!
Best,
Yao Li
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Received on Tue Oct 30 2018 - 07:30:02 PDT
