From: Francesco Pietra (
Date: Wed Jun 10 2015 - 02:24:57 CDT

Hi Felipe:
While I am still considering how to apply your suggestion to get everything
(also ligands, either already into the protein or approaching it from the
surrounding medium) in the system, do you have an idea how to apply bigdcd
scripts (rmsd centermass rgyr distance, for example) under such "broken"
conditions of the system?

Given the size of the system, I am very limited in using graphical VMD at
the computing center, so I shifted to text VMD with bigdcd (which worked
nicely with "unbroken" system", while I have no idea whether pbc commands
can be used "blindly" under text mode)



On Tue, Jun 9, 2015 at 5:10 PM, Felipe Merino <> wrote:

> Hi,
> 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.
> Best
> Felipe
> 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