VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Aug 12 2014 - 12:35:25 CDT

On Tue, Aug 12, 2014 at 1:01 PM, Natal Kanaan <kanaan_at_zedat.fu-berlin.de> wrote:
> 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?

averaged positions only make sense for structures/atoms that stay in
place, e.g. in a crystal. every part that can more more or less freely
will lead to all kinds of deformations and unphysical structures from
when being averaged over.

consider the simple example of a rotating hydrogen molecule. if it
rotates, you will get as the averaged position (over a long enough
trajectory) both atoms at the center of mass location of the molecule.

so, for your analysis, you have to carefully consider what it really
is that you want to look at. diffusing/librating/rotating water
molecules will not likely give any meaningful average.

axel.

> 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/
>>
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.