VMD-L Mailing List

From: Ahmet Bakan (lordnapi_at_gmail.com)
Date: Wed Nov 23 2011 - 21:27:45 CST

Hi All,

There is a new VMD plugin, NMWiz, which can be used to visualize (arrows
and animations) any kind of normal mode data (PCA, all atom NMA, ENM, EDA,
etc.). John has incorporated this to VMD and it will be available 1.9.1,
but it can be obtained from the links below before new VMD is released.

Plugin allows analyzing data that is loaded into VMD as a molecule (so
gromacs formats that can be analyzed, see From Molecule interface in the
documentation). The native file format for the plugin is very simple (NMD
format, see below) and can be prepared using a text editor.

Download & Installation: http://www.csb.pitt.edu/ProDy/plugins/index.html
Documentation: http://www.csb.pitt.edu/prody/plugins/nmwiz/index.html
NMD format: http://www.csb.pitt.edu/prody/reference/usage/nmd-format.html

Finally, it allows for running PCA/EDA and ANM/GNM jobs from within VMD if
you have ProDy installed. You can get it from here:
http://www.csb.pitt.edu/prody/

Best,
Ahmet

On Tue, Nov 22, 2011 at 9:13 AM, Vlad Cojocaru <
vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:

> 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>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
>>
>> 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
>> Fax: 212-849-2456
>>
>>
>>
>> On Mon, Nov 21, 2011 at 5:35 AM, maria goranovic
>> <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
>
>