VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Jul 10 2014 - 10:54:09 CDT

Hi Marco,

It sounds like you are calculating an RMSF, which VMD has direct methods
for (measure rmsf command). If you are trying to do something else, it
sounds like you already have the pseudocode you need to implement it as
a script. You would first calculate an average structure (loop over all
the frames and compute the average using the vecscale and vecsum
commands in conjunction with one another
http://www.ks.uiuc.edu/Research/vmd/current/ug/node190.html), then
subtract that average structure from each frame (using vecsub).

Take your time, read through the tcl commands in the user guide and you
should be able to solve it.
-Josh

On 7/10/14, 11:43 AM, Marco Gerolin wrote:
> Hello Josh,
> I need to subtract for each atom and for each frame of the trajectory,
> the cartesian coordinates of an average structure (I know that could
> lead to unphysical result, but I don't need any physical structure)
>
> Thank you
>
>
> 2014-07-10 17:01 GMT+02:00 Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>>:
>
> Yes. What exactly do you mean by subtract? The exact
> implementation depends on what you are trying to do.
> -Josh
>
> On 7/10/14, 10:06 AM, Marco Gerolin wrote:
>> Dear VMD users,
>> I need to subtract to a trajectory, a reference structure, for
>> each frame, is this possible in VMD?
>>
>> PS: Subtract and not align
>>
>> Thank you
>>
>> --
>> Marco Gerolin
>> Dipartimento di Scienze Chimiche
>> Università degli Studi di Padova
>> Via Marzolo 1, 35131
>> Padova
>
>
>
>
> --
> Marco Gerolin
> Dipartimento di Scienze Chimiche
> Università degli Studi di Padova
> Via Marzolo 1, 35131
> Padova