Hi All,
I have performed MD simulation for a protein in water for 60ns. With
older version I cam trajin all these file, then trajout the
trajectories in order, but with new version, the trajectories from
second mdcrd file will use the name as the first sets (prefix.number,
the number start from 1 again). So it replaced the trajectories from
the first mdcrd. So the trajectories I got is only the last set from
the last mdcrd file. Is there a solution for this?
I tried to remove water and combined those trajectory to one file.
The I extract the trajectories from the combined file. But from about
48ns, the structure got wield bond connection. I tried to extract
from the uncombined mdcrd files using the same procedure, the
trajectories are all okay. Does any had this problem? Is there any
clue for this?
Thanks,
William
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Received on Fri Jan 20 2012 - 07:30:02 PST
