From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Jun 25 2013 - 16:54:04 CDT
Hello James, the calculation of the covariance matrix has been discussed
many times in the mailing list: please search its archives.
Regarding examples of colvars configurations, there are some here:
http://www.ks.uiuc.edu/Research/namd/2.9/ug/node53.html
and here:
http://colvars.github.io/
Bests
Giacomo
On Tue, Jun 25, 2013 at 2:21 PM, James Starlight <jmsstarlight_at_gmail.com>wrote:
> 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,
>
> James
>
>
> 2013/6/25 Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
>
>> 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:
>>
>> http://www.ks.uiuc.edu/Research/namd//2.9/ug/node55.html#SECTION0001322160000000000000
>>
>> 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:
>> http://www.mpibpc.mpg.de/249995/93-ConformationalFlooding
>>
>> Giacomo
>>
>>
>> On Tue, Jun 25, 2013 at 8:52 AM, James Starlight <jmsstarlight_at_gmail.com>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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