VMD-L Mailing List

From: Ashar Malik (asharjm_at_gmail.com)
Date: Sun Oct 29 2017 - 18:27:54 CDT

This is not a problem.

Assuming everything else was correct, the wrapping will not impact your
simulation.

For visual and distance based analysis purposes if you want something you
need to "unwrap" not wrap.
See here: http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/#x1-230007

On Mon, Oct 30, 2017 at 9:26 AM, Dallas Warren <dallas.warren_at_monash.edu>
wrote:

> 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
> dallas.warren_at_monash.edu
> ---------------------------------
> 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 <stevesei_at_ku.edu> 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
>
> 

-- 
Best,
/A