VMD-L Mailing List

From: Chandra Ramananjara (mozart20d_at_yahoo.com)
Date: Thu Mar 23 2006 - 09:12:56 CST

Hi,
I was wondering how to do some VMD-style scripting within the NAMD configuration file. I would like to do some analysis based on atomic coordinates while the simulation is running. After each step of the simulation, I would like to select all the atoms, get their coordinates, and use that to calculate each atom's distance from a reference atom.
The way I've done this in the past is to dump the coordinate trajectories into the dcd file every so often (say, 100 steps) and then do the above-described analysis (in VMD) on the dcd file generated after the simulation has run. But this is no longer practical as I'm running a 1ns program (with 500,000 steps) and I would like to do the analysis after every simulation step (as opposed to after every 100 steps) so dumping the coordinate trajectory in a dcd file after every step (using dcdfreq = 1) is somewhat out of the question because this will end up generating a really huge file at the end of the simulation. Any suggestions ?

Thanks,
--Chandra
   
                
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