VMD-L Mailing List

From: Brittany Morgan (brmorgan_at_clarku.edu)
Date: Wed Mar 04 2009 - 11:21:13 CST

Hi Nicola,

I use 'pbc unwrap'.

http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/

Brittany

-----Original Message-----
From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] 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

Hi,
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 

-- 
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
E-mail: nicolag_at_chimfarm.unipg.it