VMD-L Mailing List

From: Tyler Luchko (tluchko_at_gpu.srv.ualberta.ca)
Date: Fri May 30 2003 - 15:21:40 CDT

Hi,

I've been trying to use the cartoon representation to look at the results
of an annealing simulation and I've had some inconsistent results. My
anneal run is divided up into 4 different trajectories. When I load these
trajectories into vmd I get different results from the cartoon
representation (and structure colouring). Notably, several of the beta
sheets are interpreted as random coil. This is not due to heating as
they disappear at the beginning of the heating and reappear during the
following high temperature equilibration phase. In one case, where two
frames are separated by 2 ps, one has 4 beta sheets shown and the other
has 2. The tracing of the backbones is almost identical. What might
cause this?

I have also noted that only the first frame of the dcd file seems to be
used by the cartoon representation. Is it possible that this might be
changed?

Thank you,

Tyler