VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Jun 09 2015 - 06:04:37 CDT

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