VMD-L Mailing List

From: Chris Neale (candrewn_at_gmail.com)
Date: Thu Mar 22 2018 - 10:31:06 CDT

or do a least-squared fit on the protein and then make a separate selection
for the lipid of interest and go to the trajectory tab and where it says
"now" enter "0:5:1000" to show every 5th frame from frame 0 to frame 1000
(or whatever actual time selection you want)

On Thu, Mar 22, 2018 at 9:04 AM, Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> 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
>