Re: Simulation in Collective sub-space

From: Giacomo Fiorin (
Date: Tue Jun 25 2013 - 08:03:48 CDT

Hello James, you can use the collective variables module: choose your
variables to be the eigenvectors of the covariance matrix, by providing the
code with 1) the list of atoms, 2) the 3N coordinates of the average
structure with refPositionsFile, 3) the 3N components of the essential mode
of your choice with vectorFile. You can define as many variables of type
"eigenvector" as you want:

BTW the extension of principal component analysis using metadynamics
already exists, and it's in a relatively older paper, if you're looking for


On Tue, Jun 25, 2013 at 8:52 AM, James Starlight <>wrote:

> Dear Namd users!
> I'm looking for possible way of the performing some sort of the steered
> molecular dynamics in the essential subspace (which would be organized by
> some lowest frequency modes obtained from the Principal components analysis
> of the unbiased MD trajectory for instance). Some sort of that simulation
> called as essential dynamics sampling has been implemented in Gromacs.
> Now I'm looking for possible extension of such technique which would allow
> me to perform methadynamics in collective coordinates with the Free energy
> surfaces calculation along reaction coordinates (in that case collective
> coordinates). I'll be thankful if someone provide me with some NAMD
> tutorials.
> Thanks for help,
> James

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