From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 14 2024 - 00:15:11 CST

You have to look at the c++ source code to see how g(r) is computed, the
GUI is only a frontend that collects and passes arguments to the measure
gofr or measure rdf command and displays the output computed by those
commands.

1. yes. those integrals are the same. the 4pi factor is implicit in the rho
scaling factor.
2. it is the raw histogram data collected by the g(r) algorithm. it is
returned by the measure gofr command for cases where people want to do
their own computation from that data. the GUI has to capture it, because it
is returned, but - as you noted - doesn't need it.

On Thu, Nov 14, 2024 at 12:38 AM Rajahmundry Ganesh Kumar ch20d408 <
ch20d408_at_smail.iitm.ac.in> wrote:

> 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!6KwD6i6n0KX28YMyw9T8H90e0ScJIVTwIHn_gBGXHSR67k-c4KBECYk06s4WhuB96pJ8KXoQEpX7Lzkaaw$
>>
>> Institute for Computational Molecular Science and HPC,
>> https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!6KwD6i6n0KX28YMyw9T8H90e0ScJIVTwIHn_gBGXHSR67k-c4KBECYk06s4WhuB96pJ8KXoQEpW-goanyw$
>> College of Science & Technology, Temple University, Philadelphia PA, USA
>>
>

-- 
Axel Kohlmeyer  akohlmey_at_gmail.com https://urldefense.com/v3/__https://sites.google.com/site/akohlmey__;!!DZ3fjg!6KwD6i6n0KX28YMyw9T8H90e0ScJIVTwIHn_gBGXHSR67k-c4KBECYk06s4WhuB96pJ8KXoQEpX7Lzkaaw$ 
Institute for Computational Molecular Science and HPC, https://urldefense.com/v3/__https://icmshpc.com__;!!DZ3fjg!6KwD6i6n0KX28YMyw9T8H90e0ScJIVTwIHn_gBGXHSR67k-c4KBECYk06s4WhuB96pJ8KXoQEpW-goanyw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA

image.png