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