VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Tue Aug 12 2014 - 11:49:12 CDT

No, I'm not usually interested in average structures unless I've aligned
them first. If you open up any of these trajectories individually, I'm
sure you'll find that the interesting pieces of the simulation "drift"
over time. This drift makes the literal average structure (which is what
you calculated) not a particularly useful thing to look at. To remedy
this, use an RMSD-based alignment first to eliminate the drift for your
solute, then calculate the average structure of the solute, which is
probably more like what you are after. Average solvent structure is
likely going to be messy, as even if there is a structure, the rapid
exchange is going to make it complicated to calculate.
-Josh Vermaas

On 8/12/14, 12:42 PM, 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
>>>
>