VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Mon Oct 23 2017 - 18:10:26 CDT

Don't recall of a one step way to do that.
What you can do is use the catdcd plugin.

One of its modes is to take in an index file (holding indices of atoms you
want).

http://www.ks.uiuc.edu/Development/MDTools/catdcd/

catdcd -o eq_pro.dcd -i protein.ind eq01.dcd

        Takes only the coordinates corresponding to the indices in
        'protein.ind' from eq01.dcd and writes them to eq_pro.dcd

This method will only work with a predetermined selection. So if you
know what you want to extract its good, otherwise it can't calculate
selections within cutoff etc.

If you do this -- you will need a PSF for your new (truncated) system.
Perhaps you can load your full system psf and load only one frame from
the trajectory. Make your selection and write out the PSF for it.

Again this will only work for a pre-determined selection.

On Tue, Oct 24, 2017 at 11:55 AM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Thanks Ashar. Yes the way you suggest is one way of doing it. I was just
> wandering is there any possibility of loading only a selected atom
> selection at once (without having to load the entire molecule and then
> select sub selections). Looks like your suggestion is the one to go ahead
> with.
>
> Best,
> Monika
>
> On Mon, Oct 23, 2017 at 5:05 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> Technically you don't need the entire trajectory loaded to carry out what
>> you want to do.
>> Load it in manageable portions.
>>
>> For example use first 0 last 100 step 1 to load the first 100 or however
>> many frames you want.
>> When you are done with those. use the next 100 by changing the first and
>> last flags appropriately.
>> To do the same using the GUI -- use the First and Last boxes which become
>> active when you select a trajectory for loading.
>> You can write out a few trajectories and then concatenate them using
>> catdcd.
>> I think there is another way of doing this as well but I can't recall it
>> at the moment.
>> I am assuming that was the problem and not usage of animate.
>> If this doesn't help write back.
>>
>> On Mon, Oct 23, 2017 at 7:24 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
>> wrote:
>>
>>> Hi everyone,
>>>
>>> I have a huge dcd file from which I need to write an atom selection to a
>>> separate dcd file. I need to update the selection every frame as well. To
>>> do this with animate write, I can't load the entire trajectory first as i
>>> don't have enough memory. Can someone please suggest a way to do this?
>>>
>>> Thank you.
>>> Best regards,
>>> Monika
>>>
>>> --
>>> W.A.Monika Madhavi
>>> Lecturer (Probation),
>>> Department of Physics,
>>> University of Colombo.
>>>
>>
>>
>>
>> --
>> Best,
>> /A
>>
>
>
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
> 

-- 
Best,
/A