Re: [AMBER] Trajectory

From: Thomas Cheatham III <>
Date: Tue, 23 Nov 2010 14:40:21 -0700 (Mountain Standard Time)

> To be more clear ,I am calculating as below,
> trjain md.x 4 40000 4
> strip :64-200
> diffusion :1 1 res1
> diffusion :2 1 res2

If you are trying to calculate mean-squared-displacement (which is related
to the diffusion coefficient) as opposed to root-mean-squared deviation
(which is what Simmerling was referring to) you want to use the diffusion
command. You definately do not want to do any RMS fitting since this best
fits the coordinates via rotation/translation and will remove the net
displacement. There is also no need to strip any coordinates for this

Note that the MSD for a single residue will be rather noisy; to get
reasonable diffusion coefficients for a solvent it is much better to
average over all the solvent than you follow an individual solvent
molecule. Tracking an individual residue will likely, except if done as
an ensemble average over multiple trajectories, not provide much useful
information except to suggest that one residue moves "more" than another.

Now maybe you do not want the mean-squared displacement but instead want
the atomic (or residue) positional fluctuations, such as a B-factor. For
that use the atomicfluct command and note that in this case, you likely
want to fit the trajectory to an average structure first to get the
fluctuations about the average structure...


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Received on Tue Nov 23 2010 - 14:00:04 PST
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