From: Natal Kanaan (
Date: Tue Aug 12 2014 - 11:42:05 CDT

Thanks for your quick reply Josh & John,
I got the averaged.pdb but it is a very weird structure which really can't
be used. Do you ever had that problem?

> 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:
>, 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