AMBER Archive (2009)

Subject: Re:[AMBER] How to change the input matrix for "analyze matrix" instruction?

From: һ٩ (
Date: Wed Nov 18 2009 - 10:18:51 CST

There is no way of doing that.....?
Do I have to edit the source code and recompile the system?
Thank you!

2009-11-18cyk5056 <> д
>Hi Amber users,
> I am using ptraj to get the correlation matrix of a trajectory and then use "analyze matrix" to diagonalize it. It works fine.
> However, I am now trying to analyze several trajectories and I get the average matrix of them by external software(Matlab). Then I do not know how to apply this matrix as the input of "analyze matrix" instruction. As far as I know, that instruction can only accept correlation matrix that is calculated for a certain trajectory, not matrix from outside. How can I use the matrix I made as the input of "analyze matrix"? Or any other suggestions?
> Thank you very much!!
> Best,
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