VMD-L Mailing List

From: René Hafner TUK (hamburge_at_physik.uni-kl.de)
Date: Sun Oct 25 2020 - 06:13:12 CDT

Hi Kelly,

now I see the issue here.

yeah, it might be impossible to get them all properly wrapped back as
they are not connected to each other and for me it looks the same that
box seems is too small.

But it may still work, try something like:

* qwrap center "protein and segname PROB" sel "all"

(trying to center and wrap around one specific fragment )

* qwrap center "protein" sel "all"

(use the geom center of the protein as a center and wrap all of them)

Cheers

René

On 10/24/2020 3:50 AM, McGuire, Kelly wrote:
> The pictures are described in the original post.
>
> What commands would you use to get this protein back together and
> re-centered?
>
> Also, should the same command(s) work throughout the entire 2
> microseconds (if I open all dcds at once), or will it take different
> commands depending on which segment is leaving the box at different
> times in the trajectory?
>
> /Dr. Kelly L. McGuire/
>
> /PhD //Biophysics/
>
> /Department of Physiology and Developmental Biology/
>
> /Brigham Young University/
>
> /LSB 3050/
>
> /Provo, UT 84602/
>
>
On 10/23/2020 11:15 AM, René Hafner TUK wrote:
>
> Sure just send me any Cloud link and I can have a look at the pictures
> (or via email only to me if  the image sizes are not too big.)
>
>
> I don't know about your available computing resources but from my
> experiences a Cluster generally has a few nodes with 1TB of RAM which
> would be enough. I'd try it there.
>
>
> Give the qwrap tool a try! :)
>
>
> On 10/23/2020 10:33 AM, McGuire, Kelly wrote:
>> Thanks for the response! Each DCD is about 10 GB. So, 500 GB for the
>> whole trajectory.
>>
>> Haven't ever tried qwrap. I thought it was mostly for orthorhombic
>> water box shapes.  Maybe it's worth a try.
>>
>> I couldn't attach the pictures to the first email.  Is there a way I
>> can send them to you for better context of the description in my
>> email? It might clarify the problem a bit more.  2-3 of the segments
>> are hanging outside of the water box on one side and the 4th segment
>> is hanging outside the water box on the other side. Can't seem to get
>> all segments back together in the center of the box no matter what
>> set of commands I use....
>>
>> /Dr. Kelly L. McGuire/
>>
>> /PhD //Biophysics/
>>
>> /Department of Physiology and Developmental Biology/
>>
>> /Brigham Young University/
>>
>> /LSB 3050/
>>
>> /Provo, UT 84602/
>>
>>
>> ------------------------------------------------------------------------
>> *From:* René Hafner TUK <hamburge_at_physik.uni-kl.de>
>> *Sent:* Friday, October 23, 2020 2:25 AM
>> *To:* McGuire, Kelly <mcg05004_at_byui.edu>; VMD Mailing LIst
>> <vmd-l_at_ks.uiuc.edu>
>> *Subject:* Re: vmd-l: PBC Wrapping
>>
>> Dear Kelly,
>>
>>
>> First recommendation:
>>     Use Jérôme Hénin qwrap tool for wrapping/unwrapping of trajectories.
>>
>> https://github.com/jhenin/qwrap
>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_jhenin_qwrap&d=DwMD-g&c=OCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag&r=JBqQLS7jZ5whrB0hXJY8MNYcfDrh8UhlGJ2ANxoi8s0&m=GY-WWY0PUg45_DxGX_qff9hdehVccfqfeKZVCNV-7-A&s=BsbJn-rNFL2SFSMwdf39eCuHPWfd-yTbzQjhLZzLBek&e=>
>>
>>
>> It is a lot faster than the pbctools wrap command.  (:
>>
>>
>>
>> 2. What file sizes are we talking about here? Dozens of GB or TB?
>>
>> From my point of view:
>>
>>     If you have a PC or cluster node with enough RAM it might be
>> better to load the whole 2µs DCD at once.
>>
>>
>> I'd say if the simulation ran properly regarding the Box size (NVT I
>> guess) there shouldn't be too much of a problem regarding wrapping
>> the trajectory. It might just be that the dynamics are unreasonable
>> if the protein segment interact with other parts of themselves by PBC
>> and therefore may invalidate the results.
>>
>>
>> Kind regards
>>
>> René
>>
>>
>>
>> On 10/22/2020 11:06 PM, McGuire, Kelly wrote:
>>> I know many people have asked a similar question and the topic is
>>> quite exhausted. However, I have tried multiple combinations of PBC
>>> wrap that I have found int he mailing list or in the manual and they
>>> aren't working this case.
>>>
>>> Problem Background:
>>>
>>> I just started a postdoc and have been asked to help one of the grad
>>> students to get the protein joined back together and re-centered in
>>> the water box.  He has run a 2-microsecond simulation of a
>>> multimeric protein (4 segments) in a water box. Two problems I
>>> noticed immediately is that his water box is too small for the
>>> protein (in my opinion) and second, he did not have wrap turned on
>>> in his config file.  He has chopped this 2-microsecond simulation
>>> into 40-nanosecond long DCD files, so he has 50 DCD files that need
>>> to be wrapped. In some of the DCD files I can get the protein joined
>>> back together and re-centered, but there are many that I cannot. I
>>> have pictures of one such very difficult case (email won't go
>>> through with attachments, how to send pics?).  Blue is segname PROA,
>>> Red is segname PROB, Orange is segname PROC, and Green is segname
>>> PROD. These pictures represent ~1.8-microseconds into the
>>> simulation.  Pic-1 and Pic-2 are the first frame (front and top-down
>>> views respectively). Pic-3 is the top-down view of the last frame. 
>>> All of the protein segments are constantly close to the boundary
>>> conditions.  I can only get 2-3 of the segments to join back up
>>> before centering the water box. There is always one of the segments
>>> that won't join back with the rest of the protein.
>>>
>>> Questions:
>>>
>>> 1) Is it possible to do a wrap on the whole 2-microseconds DCD files
>>> at once? Meaning load all of the DCD files and wrap the protein? Or
>>> is it better to do each DCD file individually?
>>>
>>> 2) Is this an impossible case to wrap because the water box is too
>>> small?
>>>
>>> 3) Any specific suggestions on how to get this protein put back
>>> together and re-centered?
>>>
>>> 4) In the first few DCD files, I used:
>>>
>>> pbc wrap -center com -centersel "protein and segname PROB" -compound
>>> residue -all
>>>
>>> pbc wrap -center com -centersel "protein and segname PROD" -compound
>>> residue -all
>>>
>>> pbc wrap -center com -centersel "protein" -compound residue -all
>>>
>>>
>>> This worked just fine. Why would this not work for all 50 DCD files
>>> for the whole 2 microseconds? Are different wrapping commands needed
>>> for each DCD of the same long simulation?
>>>
>>>
>>> /Dr. Kelly L. McGuire/
>>>
>>> /PhD //Biophysics/
>>>
>>> /Department of Physiology and Developmental Biology/
>>>
>>> /Brigham Young University/
>>>
>>> /LSB 3050/
>>>
>>> /Provo, UT 84602/
>>>
>>>
>> --
>> --
>> Dipl.-Phys. René Hafner
>> TU Kaiserslautern
>> Germany
> --
> --
> Dipl.-Phys. René Hafner
> TU Kaiserslautern
> Germany 

-- 
--
Dipl.-Phys. René Hafner
TU Kaiserslautern
Germany