VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Nov 22 2011 - 08:10:39 CST

On Tue, Nov 22, 2011 at 7:04 AM, maria goranovic
<mariagoranovic_at_gmail.com> 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?

have you had a look at what the IED plugin does?
http://mccammon.ucsd.edu/ied/
that is basically what you are asking for, right?
now, all you have to do is rip out the code that
does the animations/projections and make it
a standalone procedure that generates a trajectory.

axel.

> 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. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science and Technology
Temple University, Philadelphia PA, USA.