VMD-L Mailing List

From: Raul Araya (arayasecchi_at_gmail.com)
Date: Mon May 21 2012 - 09:39:45 CDT

Dear VMD users

Is there a way to use the measure rmsf command within the framework of
bigdcd?
I ask this because I know that the rmsf command will use avpos to calculate
the average position of each atom...to do this I imagine that vmd requires
to whole or at least the desired part of the trajectory to be loaded in the
memory in order to be able to compute the average position. Thus, I think
this will not work using bigdcd unless one includes in the measuring script
some way to store the average position. How can this be accomplished?

Thanks...

Raúl Araya Secchi
B.Sc Molecular Biotechnology.
Molecular Biotechnology Engineer.
PhD Student (Biotechnology Program. UNAB, Chile)
Computational Biology Lab (DLab)
Center for Mathematical Modeling (CMM)
Facultad de Ciencias Físicas y Matemáticas.
Universidad de Chile.