From: Udaya Dahal (
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).


On Sun, Mar 18, 2018 at 8:50 AM, Ashar Malik <> 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 (
> 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 <>
> 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