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.
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
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Received on Tue May 20 2014 - 05:00:02 PDT
