Re: [AMBER] cpptraj PCA PC-mode pseudo traj

From: Schröder, David Christopher <>
Date: Mon, 4 May 2020 20:52:47 +0000

Hi Daniel,
thanks for the quick answer.
Your suggestion sounds good and will result in what I was looking for.


-----Ursprüngliche Nachricht-----
Von: Daniel Roe <>
Gesendet: Montag, 4. Mai 2020 22:47
An: AMBER Mailing List <>
Betreff: Re: [AMBER] cpptraj PCA PC-mode pseudo traj


On Mon, May 4, 2020 at 4:19 PM Schröder, David Christopher <> wrote:
> I would like to know whether the exported frames between the maxima
> are real existing frames taken from the previously loaded trajectories and therefore can be labelled as representative structures.

No, they are frames generated by projecting the average coordinates along the specified eigenvector (see the manual entry for the 'modes'
command). You could potentially capture representative frames by calculating projections along the desired eigenvector (or
eigenvectors) with the 'projection' action, then filtering frames that match desired projection values (with e.g. the 'filter' action). Hope this helps,


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