[CP2K:7606] Re: how to keep the atom's trajectory within the box

Huan Wang huan... at mail.huji.ac.il
Thu Mar 24 10:07:19 UTC 2016

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,

On Thu, Mar 24, 2016 at 3:39 AM, 王胜杰 <theancientg... at gmail.com>

> 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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