VMD-L Mailing List

From: Monika Madhavi (monikamadhavi_at_gmail.com)
Date: Sun Jul 05 2015 - 23:55:29 CDT

Dear Norman,

So far the script I used worked fine. Now I want to analyze a very large
trajectory (dcd) using the same script. For small trajectories the script
worked fine since I could load the whole trajectory at once. Now because my
trajectory is very large (36 GB) my RAM (4 GB) cannot process it at once. I
tried using bigdcd but, I could not get it done. Any suggestion is greatly
appreciated.

I need to select the molecules from the initial frame and then save their
coordinates in all frames.

Thank you.

Regards,
Monika

On Thu, Mar 12, 2015 at 2:21 PM, Monika Madhavi <monikamadhavi_at_gmail.com>
wrote:

> Thanks Norman, it works perfectly!!!
>
> Monika
>
> On Mon, Mar 9, 2015 at 7:00 PM, Josh Vermaas <vermaas2_at_illinois.edu>
> wrote:
>
>> Hi Monika,
>>
>> It is possible to write out a "trajectory pdb". I think, based on the
>> documentation for the animate command (http://www.ks.uiuc.edu/
>> Research/vmd/current/ug/node121.html), that it would be something like
>> this:
>>
>> animate write pdb output.pdb beg 0 end 0 sel $sel
>>
>> The $sel writepdb version of file writing I believe can only handle one
>> frame at a time. Also, does it need to be a pdb output? A binary format is
>> going to be much smaller.
>>
>> -Josh Vermaas
>>
>> On 03/09/2015 05:26 AM, Monika Madhavi wrote:
>>
>>> Thanks Norman, your answer is exactly what I wanted. Is it possible to
>>> loop
>>> this around each frame also. Can I write the pdb entries for my
>>> atomselection ($sel here) for each frame in the same pdb?
>>>
>>> Regards,
>>> Monika
>>>
>>> On Mon, Mar 9, 2015 at 3:12 PM, Norman Geist <
>>> norman.geist_at_uni-greifswald.de
>>>
>>>> wrote:
>>>> This is not the way it should be done. It is much easier and faster to
>>>> just collect the resids you need 1st and write out the coordinates
>>>> afterwards. You can easily collect the list of resids with “lappend”.
>>>>
>>>>
>>>>
>>>> example:
>>>>
>>>>
>>>>
>>>> set myresids {}
>>>>
>>>> for {whatever} {
>>>>
>>>> if {whatever} {
>>>>
>>>> lappend myresids $resid
>>>>
>>>> }
>>>>
>>>> }
>>>>
>>>> set residlist [lrange $myresids 0 end]
>>>>
>>>> set sel [atomselect top “resid $residlist”]
>>>>
>>>> $sel writepdb my.pdb
>>>>
>>>> $sel delete
>>>>
>>>>
>>>>
>>>> Norman Geist.
>>>>
>>>>
>>>>
>>>> *From:* owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] *On
>>>> Behalf Of *Monika Madhavi
>>>> *Sent:* Monday, March 09, 2015 7:24 AM
>>>> *To:* Joaquim Rui de Castro Rodrigues
>>>> *Cc:* vmd-l_at_ks.uiuc.edu
>>>> *Subject:* Re: vmd-l: How to write coordinates to a pdb without
>>>> replacing
>>>>
>>>> existing entries
>>>>
>>>>
>>>>
>>>> Thanks Rui,
>>>> Actually I can select the residue ids I want to select but they are
>>>> selected in a random manner and the number is large. Therefore I am
>>>> wondering whether I can write coordinates of the selected molecule at
>>>> the
>>>> time it is selected without giving the whole list of ids at the end.
>>>>
>>>> Regards,
>>>> Monika
>>>>
>>>> Monika Madhavi
>>>> Department of Physics
>>>> University of Colombo
>>>>
>>>> On Mar 8, 2015 11:03 PM, "Monika Madhavi" <monikamadhavi_at_gmail.com>
>>>> wrote:
>>>>
>>>> I want to achieve the result I would get if I write this command while
>>>> looping around without writing line 2 as it is.
>>>>
>>>> set residlist {1 2 3 4 5}
>>>>
>>>> set sel [atomselect top "resid 1 2 3 4 5"]
>>>>
>>>> $sel writepdb out.pdb
>>>>
>>>> $sel delete
>>>>
>>>> Regards,
>>>>
>>>> Monik
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> On Sun, Mar 8, 2015 at 10:47 PM, Monika Madhavi <
>>>> monikamadhavi_at_gmail.com>
>>>> wrote:
>>>>
>>>> Thanks Joaquim. Actually i set N outside the loop. What i want is to
>>>> write
>>>> all the coordinates in a single pdb file. As an example, something like
>>>>
>>>> If my molecule is water,
>>>>
>>>> Resid atomname coordinates
>>>> 1 H1 .........
>>>> 1 H2 ........
>>>> 1 OH .........
>>>> 2 H1 .........
>>>> 2 H1 ..........
>>>> 2 OH .........
>>>> .
>>>> .
>>>> .
>>>>
>>>> Regards,
>>>> Monika
>>>>
>>>> Monika Madhavi
>>>> Department of Physics
>>>> University of Colombo
>>>>
>>>> On Mar 8, 2015 10:11 PM, "Joaquim Rui de Castro Rodrigues" <
>>>> joaquim.rodrigues_at_ipleiria.pt> wrote:
>>>>
>>>> Dear Monika,
>>>>
>>>> I don't quite get what you are trying to achieve... Do you want to get
>>>> separate PDB files for each resid?
>>>> Anyhow, I see a few problems with your script:
>>>> - the for loop contains a strange comparison: $i<N. I just tested this
>>>> and
>>>> it results in an infinite loop. You must set N outside of the loop.
>>>> - you're looping over resid's, but always writing to same the same file
>>>> (out.pdb)
>>>> - you're building atomselections at each iterations without deleting
>>>> them
>>>>
>>>
>>
>
>
> --
> W.A.Monika Madhavi
> Lecturer (Probation),
> Department of Physics,
> University of Colombo.
> 

-- 
W.A.Monika Madhavi
Lecturer (Probation),
Department of Physics,
University of Colombo.