Re: [AMBER] Additional random motion of com for unwrapped trajectory

From: Sourav Purohit <sour000.gmail.com>
Date: Tue, 20 May 2014 16:59:58 +0530

Thanks . . .


On Sun, May 11, 2014 at 6:30 PM, David A Case <case.biomaps.rutgers.edu>wrote:

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> 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 Tue May 20 2014 - 05:00:02 PDT