From: Nicola Giacche' (
Date: Fri May 20 2011 - 08:05:40 CDT


I have a desmond trajectory of 1.2ns, with several "jumps"...
with the command "pbc unwrap" I resolved these jumps, but not for whole
trajectory, in the last part some molecules have, again, overlong bonds
not resolved by the unwrap command.

How can I resolve this situation? I tried also to "unwrap" again but
there is not changes.

Furthermore, after the unwrap, in order to resolve the "diffusion" of
the solvent molecules, I will apply the command "pbc wrap -all -center
com -centersel "resname UNK" -compound res", but if I don't fix
completely the system with the unwrap command also the subsequent wrap
command does not resolve the "diffusion" of the solvent from the box.

I hope that there is a solution...

thanks for your help


Nicola Giacchè, PhD.
Dipartimento di Chimica e Tecnologia del Farmaco.
Faculty of Pharmacy, University of Perugia
via del Liceo 1, 06123 Perugia (Italy)
Tel +39 075 585 5169