VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 12 2014 - 10:05:56 CDT

Just to add one more option to the list Josh gave:
  On memory capacity limited machines (and ultimately all machines
are limited vs. the size of some trajectories) you can compute average
positions for "chunks" of a trajectory, and then combine those into an
overall average. You could either do it a frame at a time with something
like the "bigdcd" script, or you could write a loop that processes large
batches of frames at a time using the "measure avpos" followed by summation
into the overall average, etc. Either of those schemes could be made to work
on a machine with an arbitrary amount of memory vs. the size of the trajectory,
but they require more scripting than the other approaches.

Cheers,
  John

On Tue, Aug 12, 2014 at 10:36:49AM -0400, Josh Vermaas wrote:
> 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
> > 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/