From: Natal Kanaan (kanaan_at_zedat.fu-berlin.de)
Date: Tue Aug 12 2014 - 12:47:56 CDT

Thanks a lot to all of you for all the input.
I got into this averaged-position feature because I was trying to do what
I asked about yesterday: what I really would like to do is to re-label the
water molecules according to the distance to my protein, but I can't make
it. Any further comments would be great and thanks a lot for your time and
help.
Natal

> 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.
>