Hi,
I am trying to calculate the PMF profile for a small protein with the
end-to end distance as the reaction co-ordinate. I have stored the trj
files in NetCdf format. When I visualize the trajectories for different
windows in VMD, I see the com of the whole system moving randomly (in a
zig-zag path like a brownian particle), in addition to the fluctuations in
the atomic positions. I have used the default value of nscm. What could be
the reason for this??
Kindly help.
Thanks.
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Received on Sat May 10 2014 - 16:30:02 PDT
