I have successfully been carrying out MD simulations of an array of 10 self assembling molecules within an explicit water box at relatively short simulation times. They appear stable, so I have set up a significantly longer (for us) run of 5 ns on our university's mainframe. Looking ahead, I know this will generate a large .mdcrd file even with ntwx set higher (5000 steps) and the netCDF flag set.
In the past, I have been able to visualize the simulation using VMD on my Mac. However, if the files get much larger than 750-800MB, my computer seems to choke and is unable to complete the visualization. Are there any recommendations for visualizing larger runs? How are production runs going into the tens of ns effectively managed (filesize-wise) and visualized?
Thanks much,
Joe Bozell
University of Tennessee
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Received on Mon May 09 2011 - 13:00:04 PDT
