VMD-L Mailing List

From: SHRAVANI NETHI . (p20160500_at_hyderabad.bits-pilani.ac.in)
Date: Mon Nov 16 2020 - 07:07:46 CST

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??

Any suggestions will be highly appreciated.
Thanks in advance

Shravani