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 _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
