Re: Simulation in Collective sub-space

From: James Starlight (
Date: Tue Jun 25 2013 - 13:21:18 CDT

Hello Giacomo!

Does PCA already implemented in the NAMD ? I didnt find any tutorial of the
PCA of trajectories with NAMD.
Typically in gromacs I did covariance analysis of my trajectory (Selecting
subset of atoms excluding flexible loops) and than run dynamics in that
collective space.

Also as I understood CV module should be defined in the conf file shouldn't
it? Could you show me some example.

Thanks for help,


2013/6/25 Giacomo Fiorin <>

> 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
> ideas:
> Giacomo
> 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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