Re: [AMBER] Unit of analyze modes with ptraj

From: David A. Case <>
Date: Thu, 15 Apr 2010 17:40:51 -0400

On Thu, Apr 15, 2010, Samuel Genheden wrote:
> I have done a normal mode analysis with nmode and dumped the normal
> modes to a file. I then analyzed the modes with ptraj using
> trajin lac.pdb
> analyze modes displ file vecs end 6690 out ptraj.out
> where vecs are the file from nmode.
> My question is: what are the units of the displacements in the output file?

Nnormal mode eigenvectors are normalized in mass-weighted coordinates; the
displacement is a (unitless) number that multiplies the eigenvector, to
give an actual displacement vector (in Angstroms).

...hope this helps....dac

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Received on Thu Apr 15 2010 - 15:00:02 PDT
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