From: Dallas Warren (
Date: Sun Oct 29 2017 - 15:26:54 CDT

Not familiar with the NAMD tool, but visually you can duplicate the
periodic box in any axis direction within VMD. Graphical
Representations window, Periodic tab.
Catch ya,

Dr. Dallas Warren
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 26 October 2017 at 03:43, Seibold, Steve Allan <> wrote:
> 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