VMD-L Mailing List
From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Nov 06 2024 - 12:08:29 CST
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On Mon, Nov 4, 2024 at 7:30 PM Rajahmundry Ganesh Kumar ch20d408 <
ch20d408_at_smail.iitm.ac.in> wrote:
>
>
> 1. While calculating g(r), how bulk volume is incorporated in it ?
>
>
This is documented in the VMD user guide for the "measure gofr" command.
The g(r) GUI is just a wrapper for this command. For trajectory files that
do not contain the box volume information, it is recommended to set it
manually. There is a Utilities menu in the GUI.
Otherwise it is assumed that the system is mostly water and an estimated
volume used.
>
> 1. (as volume shows “0” )
> [image: image]
>
> Is there any source of how g(r) is calculated in VMD ?
>
Sure, the VMD source code.
> 2.How to calculate running coordination number n(r) from VMD ?
> (i.e n(r) vs r)
>
This is calculated alongside the g(r). It is just a matter of outputting it.
-- Axel Kohlmeyer akohlmey_at_gmail.com https://urldefense.com/v3/__https://sites.google.com/site/akohlmey__;!!DZ3fjg!-fu9-URxXaMl9ZFit6WPAsIwraSh5zTwOnM5oXOPVFwYSrKv5Zsa3DMr24nIF_3B5gxeCgpG0BmJWFm_QA$ Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!-fu9-URxXaMl9ZFit6WPAsIwraSh5zTwOnM5oXOPVFwYSrKv5Zsa3DMr24nIF_3B5gxeCgpG0BkYsMnaHw$ College of Science & Technology, Temple University, Philadelphia PA, USA
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