[gmx-users] combining replicate xtc files

nishap.patel at utoronto.ca nishap.patel at utoronto.ca
Tue Jun 1 19:41:38 CEST 2010


    I ran a simulation for 100ns on 2 nodes (16 cores). I tried to  
generate replicates with different starting trajectories and ran it on  
one core, so basically I have 64 replicates with different starting  
trajectories and I am using 8 nodes. I wish to combine all the .xtc  
files from each of the replicates and analyze it as a whole.xtc file.  
So I used this command :

trjcat -f *.xtc -settime -o whole.xtc (and thereafter entering 'C' to  
continue, to combine all 64 xtc files with different starting  

and I got a total of 350ns combining all the trajectories. I tried to  
get the rdf for 350ns, but the values stay lower than 1. For 100ns  
that I ran on 2 nodes I got values for rdf that fluctuate around 1. I  
tried to break-down 350ns trajectory in 100ns and I got values  
fluctuating around 1, for all set of 100ns (i.e. beginning 100ns,  
middle 100ns and last 100ns, similar to 100ns ran on 2 nodes).  
Shouldn't the rdf be constant after 100ns then? Why do my values stay  
lower than 1 for 350ns? I am not sure if I am combining the files  
incorrectly. Could anyone provide some insights?


-Nisha P

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