From: Seibold, Steve Allan (
Date: Wed Oct 25 2017 - 11:43:23 CDT

Hello vmd users.

I am using namd to simulated a protein with waters on a metal surface. The problem I am having is that at 50 ns, the metal surface atoms disappear and "reappear" in another location leaving behind a "chip" in the metal surface. I believe this is occurring as one side of the metal plate edges into the adjacent periodic box. I have been attempting to use the PBC tool to fix the problem (i.e. pbc wrap) however, I have had no success may be due to my layman's understanding to the Tcl usage.

In my NAMD simulations I am using the command "wrap all", but I am still having the metal surface's atoms migrate to the other pbc cell....

What is the best approach on how to fix this problem? I have looked in the vmd archives but following their instructions has not seemed to help with my specific problem.

Thanks, Steve