[gmx-users] Continuous trajectory processing

Aaron Fafarman aarontf at stanford.edu
Tue Apr 21 21:26:55 CEST 2009


Thanks for reading this. I'm doing many-nanosecond simulations (GMX
3.3.1) with a 2 fs time step and I would like to analyze every single
frame (or at minimum every tenth frame) of the trajectory for the
presence of a hydrogen bond to one particular atom in the simulation.
The problem with doing the analysis after the trajectory is completed
is that the trr or xtc file would contain many millions of structures
and therefore be way too large to store on our cluster even

One solution I can imagine but don't know how to implement is to have
g_hbond continuously process the trajectory file, printing the h_bond
analysis for each new coordinate set and then erasing (or never
storing) the previous coordinates. Does anyone know of an
implementation of this, or a better way to  achieve a frame-by-frame
h-bond analysis? Perhaps there is a simple unix-based file-system
approach to this (maybe using tempnam)? Thanks in advance.


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