VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Aug 12 2014 - 09:36:49 CDT

Hi Natal,

Is this running windows? If so, you are probably running into the
limitations of how much memory VMD can address (32-bit applications can
only access 4GB or so of RAM), as your DCDs are probably combined larger
than this limit. There are two solutions to this problem: only take a
subset of the frames (using step as an argument to the addfile command:
http://www.ks.uiuc.edu/Research/vmd/current/ug/node138.html), or go to a
64-bit system with sufficient RAM to load all the trajectories at once.

In terms of writing a pdb with the average structure, this should in
principle work:

set sel [atomselect $mol "whatever text you need to get the selection
you want here"]
$sel set {x y z} [measure avpos $sel]
$sel writepdb averagestructure.pdb

Be aware that the second line will change atomic coordinates for the
current frame, so instead of it being part of your trajectory, its now
the average position.

-Josh Vermaas

On 8/12/14, 7:30 AM, Natal Kanaan wrote:
> Dear all,
> I'm trying to write a pdb structure which is an average of several
> trajectories. Searching in the list, I found a script similar to the one
> below, but I don't know how to really write this new-averaged-pdb
> structure:
>
> set mol [mol new ../model8_final/setup/model8_ionized.psf type psf waitfor
> all]
> mol addfile model8_R3_parte1.dcd type dcd waitfor all
> mol addfile model8_R3_parte2.dcd type dcd waitfor all
> mol addfile model8_R3_parte3.dcd type dcd waitfor all
> mol addfile model8_R3_parte4.dcd type dcd waitfor all
> set sel [atomselect $mol all]
> measure avpos $sel
>
> Any kind of help would be really appreciated. Another issue is that, as I
> have a lot of data, if I just source this script directly in vmd, it ends
> up being "killed". I already tried with:
>
> vmd -dispdev text -e xx.tcl
>
> but it is also killed.
> Thanks a lot in advance for your help,
> Natal
>