VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Mar 16 2011 - 14:23:30 CDT

On Wed, Mar 16, 2011 at 3:12 PM, Ranyere Deyler <ranyere_at_gmail.com> wrote:
> Well, i just thought it was logical. But it seems not.
> Does anyone have a script that calculates the MSD using VMD? I don't know
> much about tcl to build one. If anyone knows about a script that does that i

then you better start teaching yourself some tcl,
if you are serious about using VMD for analysis.
since most advanced analysis processes with VMD
require customizations and you'll have to do testing
of applicability for your purposes yourself.

> would appreciate.

i am attaching what i had written a while ago for
a computational chemistry class. no warranties,
and no support. it may eat up your computer.

axel.

> Thanks a lot.
> Ranyere Deyler Trindade
>
> On Wed, Mar 16, 2011 at 12:54 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> On Wed, 2011-03-16 at 11:24 -0300, Ranyere Deyler wrote:
>> > Dear VMD users, i searched in the list for this question and i saw one
>> > or two reply but it's still not clear.
>> >
>> >
>> > What i want is to plot the MSD over time, so i can plot it and get
>> > some information over de diffusion, whether it is a superdiffusive or
>> > subdiffusive proccess.
>> >
>> >
>> > Well, namd has the "RMSD trajectory" plugin. So, theoretically i would
>> > have to get the square of the RMSD found on VMD plugin and then plot
>> > it.
>> >
>> >
>> > So i ask. Is that right? In this case, of vmd plugin, the square of
>> > the RMSD trajectory will give me the MSD?? Can i use it to look at the
>> > diffusion coefficient??
>>
>> it is a _very_ bad idea to use acronyms as a base for science.
>> the RMSD that the plugin computes is something different from
>> the MSD that you compute for self-diffusion.
>>
>> axel.
>>
>> >
>> > Thanks a lot.
>> >
>> >
>> > Ranyere Deyler Trindade
>>
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.