AMBER Archive (2006)

Subject: Re: AMBER: rms in principal component analysis

From: David A. Case (case_at_scripps.edu)
Date: Wed Jan 18 2006 - 12:52:51 CST

On Wed, Jan 18, 2006, Lydia wrote:

> (1) Should I use " rms first * " or "rms first out mwtrmsCA.dat :1-52_at_CA"
> (in my case, I need to calculate mwcovariance matrix on CA atoms and do pca
> only on CA atoms later on)? If both of them are acceptable, which of them
> you will choose in my case?

You should do the second (rms fit on the atoms you actually intend to analyze)

> (2) Have the NSCM flag in my MD simulation removed the translation or
> rotation already?

They would only remove this motion at periodic intervals; you want to remove
it at every step.

...dac

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