From: Bjørnar Jensen (
Date: Mon Feb 18 2013 - 02:04:47 CST


your selection is not complete. You're only selecting (the) parts of the
water molecules
that are within 10Å of index 6094. The selection you want to make is this:

same resid as (waters within 10 of index 6094)

I would advise you to read up on selections in the user manual.

Best regards,

On 2013-02-18 07:56, Sindrila Dutta Banik wrote:
> Dear all,
> I have a trajectory file, which I loaded into VMD. Now want to save the
> coordinates of waters within 10A separation from the substrate. I am able
> to visualize to this using the following command:
> waters within 10 of index 6094
> but as soon as I am going to save this coordinates for water which are
> with in 10A it writes few coordinate partially means one O and one H not
> the second one. How to save the coordinates completely.
> With best regards
> sindrila