(unknown charset) [AMBER] AMBER18: user-defined reaction coordinate in umbrella sampling
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?
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Received on Tue Oct 30 2018 - 07:30:02 PDT