VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Fri May 12 2006 - 02:40:59 CDT

Hi there,

I'm trying to analyze a trajectory of a complex between a big protein
and a peptide. The problem is that, when I look at some parts of the
simulation, the two parts of my system "split": the peptide is moving
to the other side of the cell --which is normal, I'm using PBC--,
while the big protein does not. The thing is that I need the complex
to stay together for the analysis -RMSD, RGYR, etc-. I've miserably
tried to put everything together, but I got nothing. Do you have any
suggestions on how to achieve this?

Thank you!

Cheers,
Michel