Re: [AMBER] Normal Mode Analysis in Amber

From: David A Case <>
Date: Thu, 22 Mar 2018 08:30:41 -0400

On Wed, Mar 21, 2018, Robert DeLisle wrote:
> I cannot, however, find any information about how to perform Normal Mode
> Analysis using Amber without running a full MD simulation first. Ideally, I
> would be able to simply run NMA and write out a trajectory file suitable
> for input to PCAsuite.

Please see Chapter 39.4, "Second derivatives and normal modes" in the
Amber 2017 Reference Manual. I'm not sure what mode format PCAsuite
requires; inside Amber, you can use the "modes" command inside cpptraj
to carry out some analyses. Of course, modes themselves are already
(mass-weighted) principal components.

...hope this helps....dac

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Received on Thu Mar 22 2018 - 06:00:02 PDT
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