From: Axel Kohlmeyer (
Date: Mon Nov 16 2020 - 07:42:46 CST

On Mon, Nov 16, 2020 at 8:35 AM SHRAVANI NETHI . <> wrote:

> Dear vmd users,
> I have been trying to find the dynamics if water between clay layers.
> I selected the water between layers using "exwithin".
> The water molecules keep on changing between these layers during
> simulation.
> When i am trying to save the updated coordinates of these dynamic water
> molecules that does not remain same at each time frame into new pdb file
> using save coordinates in vmd, i found that the coordinates of only those
> water molecules selected at definite timeframe are being saved throughout
> trajectory.
> How can save coordinates of those water molecules that are present between
> layers with updation of trajectory i.e. the water molecules that are not
> fixed and keep on change between layers with trajectory updation??

you have to do this in a loop writing out a single file for a single frame
and with updating the selection in between.
updating a selection is a costly operation and thus it is only done when
explicitly requested.


> Any suggestions will be highly appreciated.
> Thanks in advance
> Shravani

Dr. Axel Kohlmeyer
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.