VMD-L Mailing List

From: Joyce Tan (joyce.tankh_at_gmail.com)
Date: Mon Sep 27 2010 - 04:58:48 CDT

Hi.

I've extended my 5ns MD simulation for another 10ns using GROMACS. After the
simulation completed, i've converted some of the trajectory frame into pdb
format and the protein appear to break into parts as in the attached jpeg
file. When I look back to the trajectory file, the protein is broken into
parts, too with long lines connecting the parts. May I know why this occur
and how to solve it?

Thanks.

Regards,
Joyce


6ns.jpeg