Re: PCA calculation

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Tue Feb 12 2008 - 10:24:33 CST

Dear Richard,
it was a reference to xkcd (http://xkcd.com/378/), a relatively popular
webcomic. You may have noticed the indication that my comment was a joke
at the end of the line. If I had the matlab script I used to do pca
handy, I would have posted it as well.

Personally, I found the number of different solutions posted in this to
be quite useful and encouraging; we've had references to two standalone
programs which do pca for you, and instructions for importing dcd data
into two different numerical computing environments. People can choose
the solution that best matches their intent and personal skills.

Peter

Richard Wood wrote:
> What gets me in this thread is the "implication" that one has to be
> able to write code in order to do MD, use NAMD, do PCA or, better yet,
> even be a computational chemist.
>
> Personally, I'd rather know why H2O is a liquid and H2S isn't than to
> be able to "write code".
>
> A person that knows why water is a liquid when it shouldn't be is a
> chemist (or physicist) while the latter is a programmer.
>
> Those of you that want to imply we should all be able to write code
> should go and be on another list.
>
> A REAL chemist uses the code (or program) that helps him to be solve
> the particular problem he's working on or is interested in.
>
> We're not all programmers on this list.
>
> Good grief.
>
> I've done PCA and I used NAMD to do my MD and used a script written in
> Matlab.
>
> Richard
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959
> woodx278_at_umn.edu
>
>
> ----- Original Message ----
> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
> To: "Xu, Jiancong" <xuj1_at_ornl.gov>
> Cc: ramya narasimhan <ramya_jln_at_yahoo.co.in>; namd-l_at_ks.uiuc.edu
> Sent: Monday, February 11, 2008 10:38:15 AM
> Subject: Re: namd-l: PCA calculation
>
> *Real* programmers use matdcd
> (http://www.ks.uiuc.edu/Development/MDTools/matdcd/) and do it in
> matlab. ;-)
> But gromacs is the fast and easy way way.
> Peter
>
> Xu, Jiancong wrote:
> > Don't think so. One thing you can do is to convert dcd trajectory to
> any other format that can be read by gromacs, and use gromacs to
> calculate PCA.
> >
> > Jiancong
> >
> >
> > -----Original Message-----
> > From: owner-namd-l_at_ks.uiuc.edu <mailto:owner-namd-l_at_ks.uiuc.edu> on
> behalf of ramya narasimhan
> > Sent: Mon 2/11/2008 2:49 AM
> > To: namd-l_at_ks.uiuc.edu <mailto:namd-l_at_ks.uiuc.edu>
> > Subject: namd-l: PCA calculation
> >
> > Hi all,
> > Is it possible to calculate PCA for MD trajectories using
> NAMD?
> > Thanks in advance.
> >
> > Ramya.L.
> >
> >
> > ---------------------------------
> > Chat on a cool, new interface. No download required. Click here.
> >
> >
>
>
>
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