From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Sun Mar 18 2018 - 09:44:33 CDT

Sorry, I didn't put my question properly. I didn't mean to calculate
distance. I want to calculate the correlation. I have 'n' water molecules
within distance 'd' of a fixed point say (0,0,0). Now in subsequent frames,
how many of them(water molecules in initial frame 'n') stay within that
distance 'd' from (0,0,0).

Regards,

On Sun, Mar 18, 2018 at 8:50 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Do you mean you want to measure/monitor the distance between "a molecule
> A" and a "water molecule" in your simulation? The word trajectory update is
> confusing.
>
> If you just want a distance between two molecules listed for every frame
> of your trajectory -- then you should know that a distance can only be
> calculated between two points. Molecules have more than 1 point point so
> you will have two decide which point to use as reference. You can choose an
> atom or select a centre of geometry/mass and measure distance between that
> for two molecules.
>
> To measure distance look at the command measure bond (
> http://www.ks.uiuc.edu/Research/vmd/vmd-1.8.6/ug/node124.html)
>
> For this I don't think you can use anything else apart from atoms, meaning
> this won't work with centre of mass/geometry.
> Try this. Drop back if it doesn't work and someone can help more. This is
> obviously assuming I understood your problem correctly.
>
>
>
> On Sun, Mar 18, 2018 at 7:31 PM, Udaya Dahal <dahal.udaya_at_gmail.com>
> wrote:
>
>> Hi,
>>
>> I would like to extract the data as in visualization without trajectory
>> update. For eg. I am looking at water molecules at some distance from
>> another molecule A. If I don't update the trajectory, I can see the water
>> moving away from the initial distance. How to extract this data in text
>> mode? I appreciate your help.
>>
>> Regards,
>> UD
>>
>
>
>
> --
> Best,
> /A
>