VMD-L Mailing List

From: Oliver Beckstein (orbeckst_at_jhmi.edu)
Date: Tue Nov 20 2007 - 14:28:45 CST

Hi,

is there a way to analyse trajectories that are bigger than the
available RAM? For instance, I have trajectories > 5GiB in size that I
would like to analyze with VolMap but they can't be loaded because VMD
insists on keeping the whole trajectory in memory.

A cumbersome work-around would be to split the trajectory into smaller
chunks, run volmap on each chunk, then average the resulting dx files.
However, I can think of situations when a simple average is not enough
(for instance for time correlation functions) and it would very
convenient if one could just have a (python-style) iterator over a
trajectory (similar to the 'for timestep in universe.dcd: ....' idiom
in http://code.google.com/p/mdanalysis/ ).

(Note: I don't think that increasing swap space is a solution because
that leads to the computer almost grinding to halt when the trajectory
is loaded.)

Thanks,
Oliver 

--
Oliver Beckstein * orbeckst_at_jhmi.edu
Johns Hopkins University, School of Medicine
Dept. of Physiology, Biophysics 206
725 N. Wolfe St
Baltimore, MD 21205, USA
Tel.: +1 (410) 614-4435