Re: [AMBER] Trajectory

From: John S <>
Date: Tue, 23 Nov 2010 18:04:31 -0500

Thank You for your suggestion.I can use atomicfluct to get the deviation
from the the average structure.
Here I need to calculate the diffusion coefficients of selected residues too
So I plan to calculate this from the slope of Mean Square Deviation plots
over the a selected part of trajectory (which is a range of 5000ps).

I am not calculating diffusion of solvent , but of selected residues of my
structure (in all 5 residues).
Yes the MSD trajectory is noisy, will I get meaningful results out of this
analysis of diffusion coefficients


On Tue, Nov 23, 2010 at 4:40 PM, Thomas Cheatham III <> wrote:

> > 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
> calculation.
> 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...
> --tec3
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Received on Tue Nov 23 2010 - 15:30:02 PST
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