On Sun, May 11, 2014, Sourav Purohit wrote:
>
> 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??
Without knowing any details, what you describe sounds like what is expected.
Changes in the com won't by themselves have any effect on an internal
measurement like the end-to-end distance.
...dac
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Received on Sun May 11 2014 - 06:30:02 PDT
