VMD-L Mailing List

From: Rajahmundry Ganesh Kumar ch20d408 (ch20d408_at_smail.iitm.ac.in)
Date: Wed Nov 13 2024 - 23:38:36 CST

Thanks Axel! and Diego! for the valuable insights & suggestions,

i ve gone through the source code of g(r) gui !, Though the code has five
entities which is * rlist , glist, ilist , hlist* and* frlist *, the
output file is printing only the first three.
I want to know a few things here*!*
*1 . * The third list "ilist" is given as the number integral of g(r)
i.e * int [0 to r ] row. g(r) . r^2* in the documentation. where as the
running coordination number is defined as
[image: image.png]
does the third list multiplied by 4 . pi is the coordination number(CN)

2. regarding *hlist *
   What does an unnormalised histogram mean ? Could you please elaborate
more on this !
Thanks
Ganesh

On Wed, 6 Nov, 2024, 11:38 pm Axel Kohlmeyer, <akohlmey_at_gmail.com> wrote:

>
>
> 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!5nJmwmn6IvnxvA34u3OONtUK8Is7Aie1ux9vQLRjuxdv0fNiI-9jhuTfdHpXX-dV-obbkzhO7Dg0k06TGZ2R0amSnw$
> Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!5nJmwmn6IvnxvA34u3OONtUK8Is7Aie1ux9vQLRjuxdv0fNiI-9jhuTfdHpXX-dV-obbkzhO7Dg0k06TGZ1JAvyX2g$
>
> College of Science & Technology, Temple University, Philadelphia PA, USA
>


image.png