VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Sep 17 2015 - 09:32:23 CDT

What was the pbc unwrap command used? If I want something specific in
the center, I tend to use the wrap algorithm. Unwrap is a simple
algorithm, and looks atomically between trajectory frames to see if a
single atom moved more than half the box length. If so, it moves it back
so that the atom does not move more than a single PBC image from one
frame to the next. For fast-moving molecules like water, oftentimes the
algorithm breaks up molecules if it moved approximately half the box
length. If you need it unwrapped, I think the simplest thing to do would
be to only run the unwrap command on a reduced atomselection ("not
water" for instance).

-Josh Vermaas

On 09/16/2015 04:34 AM, Sourav Ray wrote:
> Hello
>
> After running simulation of a peptide molecule for 30ns (2fs times
> steps) under periodic box and NVT conditions. Upon unwrapping the
> atoms, I am getting bonds between certain atoms as elongated lines,
> the probable reason being one atom of the bond is in one periodic box
> and the other in the next one.
>
> Can someone please suggest any remedial action so that I may extract
> normal bond visualizations after the necessary processing.
>
> Thanks and regards
> Sourav Ray