From: Sunyeping (
Date: Sat Jan 03 2015 - 09:13:16 CST

Dear all,I  want to show all water molecules within 3.5A of a particular residue in the protein through out a MD trajectory in VMD. In  Graphical representations dialogue box, I created a representation with the atom selection being "water and within 3.5 of segname P3 and resid 3". This operation did show water molecules around this protein residue, but this atom selection applied just to the frame which was showed in VMD when the atom selection was made but not for all the frame. When I changed the frame showed in VMD, I could observe these water molecules left far away from that protein residue. So how can I show just the water molecules around the reside for all the frames?   Yeping Sun Institute of Microbiology, Chinese Academy of Sciences