[gmx-users] Continuous trajectory processing

XAvier Periole x.periole at rug.nl
Tue Apr 21 22:43:53 CEST 2009

you have the choice of using the -dt XX option of g_hbond which will
tell to analyze only every XX structure. I am not sure this is present  

the other way is to use trjconv with the dt option again an write the
frames every XX steps.

On Apr 21, 2009, at 9:26 PM, Aaron Fafarman wrote:

> Hello,
> 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
> temporarily.
> 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.
> -Aaron
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