[CP2K:7613] Re: how to keep the atom's trajectory within the box

[Huan Wang]

Hi Shengjie,

VMD is able to load short segment of the trajectory. You do not need to
load the whole trajectory if the file is larger than the memory of your
computer.

Since you have known the possible step point that the atom might move out
of the box based on your own program (script), it is a good idea to check
the trajectory around this point by using VMD.
For example, if the step point is the 23456th frame, you can only load 100
points before and after this frame. e.g. from 23356 to 23556. Please see
the picture below on which the red box and ellipse indicating the key
points you need to pay attention.

[image: Inline image 1]

After loading the segment of your trajectory, you need to set the pbc box
length and wrap the atoms as I suggested in the last response.
Visualization the results will help you check both the trajectory and your
program (script).

Good luck.

Huan
.



On Thu, Mar 24, 2016 at 5:37 PM, 王胜杰 <theancientg... at gmail.com>
wrote:

> Dear Huan,
>
> I didn't display the trajectory, because the trajectory file is really
> big, thus it can't be dragged to VMD.  I wrote a little program
> to identify it. First I found the min and max coordinates in the initial
> configuration, in ensemble NVT, when the atom coordinates less than min or
> larger than max, identify it crossing the boundary. And print out which
> atom and during which step.
> Sure I can split the trajectory into several parts, but splitting costs
> too much time, and VMD always crash.
>
> Best wishing,
> Shengjie Wang
> .
> 在 2016年3月24日星期四 UTC+8下午6:07:21，Huan Wang写道：
>>
>> Hi Shengjie,
>>
>> An additional question is how do you display the trajectory?
>> If you use VMD, then you need to type some codes in *Extensions --> Tk
>> console* to let the VMD know the size of your simulation box.
>>
>> The codes are:
>>
>> pbc set {xxx xxx xxx} -all
>> # Here the "xxx" is the length of your (cubic) box. And "-all" means
>> this operation controls all frames in the current trajectroy.
>> pbc box
>> pbc wrap -all
>> # The wrap commend will show the atoms on the other side of the box when
>> atoms move out of the box.
>>
>> Good luck,
>> Huan
>> .
>>
>> On Thu, Mar 24, 2016 at 3:39 AM, 王胜杰 <theanci... at gmail.com> wrote:
>>
>>> Hi Huan,
>>>
>>> Thanks for your attention.
>>> Yes, I did. I noticed and added the keyword the PERIODIC, and I tried
>>> the ensemble NPT_I and NVT, but cp2k still printed a real trajectory.
>>>
>>> Regards,
>>> Shengjie Wang
>>>
>>> 在 2016年3月23日星期三 UTC+8上午4:45:33，hua... at mail.huji.ac.il写道：
>>>
>>>> Hi Shengjie,
>>>>
>>>> Did you specify the keyword PERIODIC in the &SUBSYS &CELL section?
>>>> Please see the CP2K manual
>>>>
>>>> https://manual.cp2k.org/cp2k-2_6-branch/CP2K_INPUT/FORCE_EVAL/SUBSYS/CELL.html#PERIODIC
>>>>
>>>> Regards,
>>>> Huan
>>>> .
>>>>
>>>> On Friday, March 18, 2016 at 6:41:41 PM UTC+2, 王胜杰 wrote:
>>>>>
>>>>> Dear all
>>>>>
>>>>> When I was dealing with the trajectory of MD, I found the atoms always
>>>>> move beyond the boundary, making some atoms' coordinate larger than the box
>>>>> length,which reflect the true trajectories.
>>>>> But I don't want a true trajectory, I want a periodic boundary.When
>>>>> the atoms cross the boundary, the coordinate will minus the box length
>>>>> automatically, which each direction of  atoms' coordinate is less than the
>>>>> box length. By adding what command line can I fix that?
>>>>>
>>>>> Thanks in advance.
>>>>> Shengjie Wang
>>>>>
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