On Tue, 2014-05-20 at 07:30 -0400, Jason Swails wrote:
> On Tue, 2014-05-20 at 12:59 +0400, James Starlight wrote:
> > Dear Amber users!
> >
> > Recently I've performed test NPT simulation ( below you can see details of
> > setup) of my water soluble protein. During analysis of the production
> > trajectory I've noticed constant rigid-body-like diffusion of my protein
> > across boundaries of PB (molecule crossed box boundaries many time). How I
> > could avoid of this ? Does the iwrap = 1 flag influence on such behavior ?
>
> Yes, iwrap=1 causes molecules to be wrapped back into the "central" unit
> cell if they leave. You can use the "unwrap" command in cpptraj to
> reverse wrapping if you want to study diffusion properties.
One other comment. I don't think you were trying to study diffusion,
but if you were you would need to run constant energy (not constant
pressure or temperature) in order to get meaningful results.
>
> If you want to eliminate the "appearance" of your protein moving across
> periodic boundaries, you can use the "autoimage" command in cpptraj to
> image your system so that the protein is always at the center of the
> box.
>
> HTH,
> Jason
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 20 2014 - 05:00:03 PDT
