VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Nov 22 2011 - 08:13:29 CST

I.E.D. (Interactive Essential Dynamics) should still be a good piece of
code to visualize PCA modes from ptraj and gromacs ...
I know it requires (or at least used to require) source compilation of
VMD and I also know its not being developed further (pity) but I find it
good for visualization purposes.

If somebody asks me what feature I am missing in VMD, is the
incorporation of IED as a standard plugin or the development of an
alternative plugin that can be accessed through the Extensions menu in
VMD ... Maybe even a PCA calculator would be quite nice ... I also know
the answer to this question could be another question: why don't I
develop such a tool ? I wish I had the time to do it ....

And then movies can be created with the VMD movie maker plugin.

Best,
Vlad

On 11/22/2011 01:04 PM, maria goranovic wrote:
> Hi Davide
>
> Thanks for the help. I was hoping to write or get help writing
> something more flexible within vmd as a script, since the eigenvectors
> and eigenvalues are already calculated. I was wondering if there were
> other suggestions?
>
> Thank you all
>
>
> On Mon, Nov 21, 2011 at 7:37 PM, Davide Provasi
> <davide.provasi_at_gmail.com <mailto:davide.provasi_at_gmail.com>> wrote:
>
> Maria- I'm not sure whether this is the easiest way,
> but you can do it using the R bio3d package
> http://mccammon.ucsd.edu/~bgrant/bio3d/html/mktrj.pca.html
> <http://mccammon.ucsd.edu/%7Ebgrant/bio3d/html/mktrj.pca.html>
>
> good luck
> Davide
>
>
>
> --
> Davide Provasi
> Dept. of Structural and Chemical Biology
> Mount Sinai School of Medicine
> Icahn Medical Institute Building
> 1425 Madison Avenue, Box 1677
> New York, NY 10029-6574
> Tel.:212-659-8618 <tel:212-659-8618>
> Fax: 212-849-2456 <tel:212-849-2456>
>
>
>
> On Mon, Nov 21, 2011 at 5:35 AM, maria goranovic
> <mariagoranovic_at_gmail.com <mailto:mariagoranovic_at_gmail.com>> wrote:
> > Hi
> > I used g_covar in the GROMACS utility to come up with a series of
> > eigenvectors and eigenvalues for my protein trajectory. How does
> one make a
> > movie of this in vmd?
> > --
> > Maria G.
> > Technical University of Denmark
> > Copenhagen
> >
>
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen 

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de