VMD-L Mailing List

From: Amir (amirsuhail029us_at_gmail.com)
Date: Mon Feb 19 2024 - 12:49:35 CST

Thank you.

Best regards,
Amir Suhail

On Mon, 19 Feb 2024 at 07:55, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> Make sure that your trajectory file contains box information and then you
> should be able to use "pbwithin" instead of "within".
>
>
> On Mon, Feb 19, 2024 at 2:20 AM SHIVAM TIWARI <t.shivam_at_iitg.ac.in> wrote:
>
>> I am not sure though, but unwrapping the trajectory and then doing the
>> analysis may get the desired result.
>>
>> Just type : "pbc unwrap" in the tkconsole after loading your trajectory
>> to unwrap.
>>
>> Regards,
>> Shivam
>>
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>> ------------------------------
>> *From:* owner-vmd-l_at_ks.uiuc.edu <owner-vmd-l_at_ks.uiuc.edu> on behalf of
>> Amir <amirsuhail029us_at_gmail.com>
>> *Sent:* Monday, February 19, 2024 2:24:49 AM
>> *To:* vmd-l_at_ks.uiuc.edu <vmd-l_at_ks.uiuc.edu>
>> *Subject:* vmd-l: atomselection near periodic boundaries
>>
>> You don't often get email from amirsuhail029us_at_gmail.com. Learn why this
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>> Dear all,
>>
>> I am doing some calculations on the Lammps trajectory, for which I need
>> to find all information of neighbors within a cutoff around every bead. My
>> code works fine for all the polymers (bead-spring model), which are well
>> within the box. I am finding neighbors around a bead as follows:
>>
>>
>> set sel [atomselect top “within 3 of index 10”]
>>
>>
>> Suppose my bead (say index 10) is at the edge of the box, and the polymer
>> and some other chains are crossing the boundary and appearing from the
>> other side. This atom selection is not capturing all the neighbors,
>> considering periodic boundaries. It is only giving me the beads around the
>> edge, not from the other side, which are within cutt-off of my bead of
>> interest considering periodic boundaries. Is there a way to get all the
>> neighbors for edges? Thank you in advance.
>>
>> Best regards,
>> Amir
>>
>
>
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__https://goo.gl/1wk0__;!!DZ3fjg!6sdmr_lRKCJtGgtIP8k6FdEbsYESuvr9d6KyHHBXmjAe7xBcYe8YL9Hc3Gl5DwK9qIO-s_qfEI-PXA3I3alWOjbPuSc$
> Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!6sdmr_lRKCJtGgtIP8k6FdEbsYESuvr9d6KyHHBXmjAe7xBcYe8YL9Hc3Gl5DwK9qIO-s_qfEI-PXA3I3alWZYqYHxs$
>
> College of Science & Technology, Temple University, Philadelphia PA, USA
>