Quite likely, it is due to part of molecule moving "out of box". Also,
the molecule could be of multiple chain.
So you need to find a way to put the whole molecule in one piece. Try
various options from trjconv -pbc. If it is DNA, a trick is to define
one chain as an index group and then center that group.
Regards,
Yang Ye
Anamika Awasthi wrote:
Dear All,
Please tell, what should I predict from this graph?
I can understand this is normal type of graph.
Sorry for inconvenience, but I want to ask some questions,
my this job crashed many time, because of power shut down and I had to
restart this again and again, I used tpbconv for the same.
but now when I was trying to get rmsd plot from my running job..its
not reading the tpr file, which I got from tpbconv , its reading
previous tpr file.
Is it okey?
Thanks in advance
Anamika
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