VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Feb 01 2012 - 10:41:58 CST

Hi,
  You can use VMD to extract information from your trajectory and
generate new files that you can more easily read into tools like R
or Mathematica if that's what you wish to do.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Feb 01, 2012 at 05:26:44PM +0100, Hitesh Patel wrote:
> Thanks,
> Yes, I meant to say PCA. I am well experienced with R and matlab. But,
> desmond trajectory files are binary files. How can I read trajectories in
> R or matlab?? Can you please send any tutorial link or something like
> that?
> While Searching for tool, I saw in some papers it was mentioned they, used
> R package called Bio3D. But, in that also it does not identify desmond
> trajectory files.
>
> Regards,
>
> Hitesh Patel
> On Wed, Feb 1, 2012 at 5:18 PM, SAPAY Nicolas 232321
> <Nicolas.SAPAY_at_cea.fr> wrote:
>
> If by PCA you mean "Principal Component Analysis", two popular tools for
> this kind of statistical analysis are R and Mathematica.
>
> Nico
>
> --
> [ Nicolas Sapay ]
> Molecular Modeling and Biocomputing
> Commissariat `a l'Energie Atomique - Grenoble, France
> Tel : +33 (0)4 38 78 48 48
> ________________________________________
> De : owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] de la part de
> Hitesh Patel [hiteshpatel379_at_gmail.com]
> Date d'envoi : mercredi 1 fevrier 2012 16:29
> A : vmd-l_at_ks.uiuc.edu
> Objet : vmd-l: PCA of desmond trajectories
>
> Hello All,
>
> sorry to ask question not regarding VMD. I have desmond trajectories.
> And I want to do PCA of that. Could you please suggest me any tool for
> PCA of desmond trajectories?
> Thanks,
>
> Regards,
>
> Hitesh Patel 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078