From: Brittany Morgan (
Date: Wed Mar 04 2009 - 11:21:13 CST

Hi Nicola,

I use 'pbc unwrap'.


-----Original Message-----
From: [] On Behalf Of
Nicola Giacche'
Sent: Wednesday, March 04, 2009 11:15 AM
To: VMD Mailing-List
Subject: vmd-l: script to resolve trajectory "jumps" on Desmond dynamic

I would to resolve a problem of Desmond dynamic... in some frames of the
dynamic, when an atom of the protein goes beyond the water-box, the
protein "jumps" to the next water-box... precisely, if the atom goes
beyond the Y direction, the component Y of the coordinates of the
protein "jumps" of value of the lenght Y of the water-box.

Is there a script on VMD able to restore the correct Y coordinates of
the protein (or chain), automatically, in the frames with the "jumps"?

thanks in advance,

Nicola Giacchè,
PhD Student
Bachelor Degree in Medicinal Chemistry and Technology of Drugs
University of Perugia
Department of Medicinal Chemistry and Technology of Drugs
Via del Liceo, 1 - 06123 Perugia (Italy)
Tel ++39 075 585 5169/5156