VMD-L Mailing List

From: Natal Kanaan (kanaan_at_zedat.fu-berlin.de)
Date: Tue Aug 12 2014 - 12:01:02 CDT

Hi,
yes, I already wrapped the dcd before, so I thought the problem was
solved. Maybe I need to write a new dcd aligned or something like that?
Thanks a lot,
Natal

> I assume ran a periodic simulation, so you're also going to have to deal
> with PBC unit cell coordinate wrapping issues. This is best done by
> having
> a look at the "pbctools" VMD plugin and doing preprocessing on your
> structure
> prior to averaging coordinates.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Aug 12, 2014 at 06:42:05PM +0200, Natal Kanaan 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
>> >>
>> >
>>
>
> --
> 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/
>