From: Felipe Merino (
Date: Tue Jun 09 2015 - 10:10:30 CDT


I remember that for this kind of problems you have to first unwrap the
simulation (pbc unwrap -sel protein for example) and later re-wrap it
around your protein. That should give you a unit cells centered around
you intact tetramer.


On 09/06/15 13:04, Francesco Pietra wrote:
> Hello:
> During NAMD MD with a large homotetramer, at ca 250ns a small portion
> of the tetramer is out of the TIP3 box. At ca 300ns one of the
> subunits splits out of the other three. It appears to be an artifact
> of contiguous boxes, however the below command (VMD 1.9.2 remote
> visualization from the computing center)) does not recompose the
> homotetramer
> pbc wrap -all -compound res -center com -centersel protein
> pbc box
> The additional complication is that I am monitoring ligands that from
> the surrounding medium penetrate the cavities of the protein to the
> active center occupied by the substrate.
> Thanks for suggestion how to recompose the homotetraner
> francescp pietra