VMD-L Mailing List

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Thu Mar 22 2018 - 10:04:10 CDT

My suggestion would be to use two selections, one for the protein and one
for the cholesterol molecule, compute the center of mass of each using
measure center, compute the difference between the two using vecsub, and
transform the three Cartesian components into whatever you like.

The VMD guide has examples of custom Tcl scripts that you can look at.

Giacomo

On Thu, Mar 22, 2018 at 2:56 AM, Shashank Ranjan Srivastava <
sranjan_at_iiserb.ac.in> wrote:

> Hello Fiorin,
>
> In my simulation assembly I have added cholesterol molecule now I want to
> see cholesterol positioning around the protein (beta barrel) with respect
> to time.
>
> So how can I calculate change in positioning of cholesterol molecule from
> geometric centre of my protein barrel and map it in two dimensional form
> that how cholesterol Is moving around the barrel with respect to time.
>
> Thank You
>
> On Wed, Mar 21, 2018 at 7:36 PM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Hi, can you explain more precisely what you are trying to do?
>>
>> You may find this useful if you need help with the coordinate
>> transformation:
>> https://en.wikipedia.org/wiki/Cylindrical_coordinate_system
>>
>> On Wed, Mar 21, 2018 at 2:16 AM, Shashank Ranjan Srivastava <
>> sranjan_at_iiserb.ac.in> wrote:
>>
>>> Hello everybody,
>>>
>>> Can anyone please help me out regarding 2-dimensional mapping of a
>>> particular lipid molecule around the geometric centre of protein molecule
>>> in protein-lipid assembly.
>>>
>>> Thank You
>>> --
>>> Shashank Ranjan Srivastava
>>> Molecular Biophysics Laboratory
>>> Department of Biological Sciences,
>>> IISER-Bhopal,
>>> Madhya Pradesh
>>>
>>>
>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
>
> --
> Shashank Ranjan Srivastava
> Molecular Biophysics Laboratory
> Department of Biological Sciences,
> IISER-Bhopal,
> Madhya Pradesh
>
> 

-- 
Giacomo Fiorin
Associate Professor of Research, Temple University, Philadelphia, PA
Contractor, National Institutes of Health, Bethesda, MD
http://goo.gl/Q3TBQU
https://github.com/giacomofiorin