(unknown charset) [AMBER] AMBER18: user-defined reaction coordinate in umbrella sampling

From: (unknown charset) 李耀 <liyao17.mails.tsinghua.edu.cn>
Date: Tue, 30 Oct 2018 22:06:20 +0800 (GMT+08:00)

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
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