Re: PCA and vector

From: Dhiraj Srivastava (
Date: Sat Jun 16 2018 - 13:03:57 CDT

Thanks Jérôme
                          I figured out how can i get the vector. Its in nmwiz output file.

Sent from my iPhone

> On Jun 16, 2018, at 9:13 AM, Jérôme Hénin <> wrote:
> I don't know the specifics of NMWiz, but once you obtain the vector, you can use it within an 'eigenvector' coordinate in Colvars to do the steering.
> Your second question is risky for anyone to answer. I can only say that system knowledge is very important.
> Jerome
>> On 15 June 2018 at 20:59, Dhiraj Srivastava <> wrote:
>> Hi all
>> I have done some MD simulation and principal component analysis using NMWiz. Now I want to extract out the vectors corresponding to some of the mode (for a group of atom) and use them for steered MD. How can I do that? also in the absence of any information about conformation change, is it reasonable to do steered MD in the direction of principal components?
>> Thanks
>> Dhiraj

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