Hello,
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
time/trajectory)
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?
Thanks.
-Nisha P
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.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 gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
