VMD-L Mailing List

From: Cesar Millan (pachequin_at_gmail.com)
Date: Tue Aug 12 2014 - 12:15:11 CDT

that is completely normal, you need to minimize the final average structure
for a few steps.

Regards

############################
César Millán Pacheco
Facultad de Ciencias
Universidad Autonoma del Estado de Morelos
Tel: 777 3297020
Fax: 777 3207040
email: cmp_at_uaem.mx
          pachequin_at_gmail.com

On Tue, Aug 12, 2014 at 11:42 AM, Natal Kanaan <kanaan_at_zedat.fu-berlin.de>
wrote:

> 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?
> Thanks,
> Natal
>
> > 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
> >>
> >
>
>
>