From: Elias Ahadi (
Date: Wed Jul 21 2010 - 12:26:08 CDT


I have a problem in displaying a simulation in VMD. My trajectory file is in PDB format and contains 2500 frames. My simulation consists of 1000 waters, 4 ions and a model protein chain. When I open my trajectory file, VMD seems to display an "extra line" between 2 water molecules that are on opposite sides of the water cluster. I display the waters as LINE and other constituents as VDW representations. This problem disappears if I display all the atoms in VDW format.

The other odd thing is that if I extract 1 frame of my simulation and copy it to a blank PDB file and open that with VMD, it does not display the "extra line" between the 2 waters even in LINE format.

Has anyone else out there come across this problem and if so is there a solution to this.

Really appreciate if anyone has some ideas.