AMBER Archive (2006)

Subject: Re: AMBER: Mass weights

From: Thomas Cheatham (
Date: Mon Nov 06 2006 - 22:58:54 CST

> I've been using ptraj command atomicfluct. As it is implemented in the
> algorithm, options bymask and byres of this command dump the results in
> mass-weighted manner. I would appreciate it very much if someone could give me
> a reference to the reason/s for the use of mass weighted values for the groups
> of the atoms. Any information/reference will be enormously appreciated.

Given that no one else is responded, I provide my rational; but wonder
up front why we should calculate these values without mass weighting?

I implemented this originally, based on other codes and common practice,
to allow comparison of observed atomic fluctuations to those measured
experimentally. [Note that if you look back in the archives, you can see
a critical error that has since been resolved in that calculated B-factors
are mean squared displacements, whereas atomic positional fluctuations are
not squared (previously both were not squared, hence ptraj calculated
B-factors were too large).]

Comparing to experiment, the fluctuations are mass-weighted. As the
method is extended to residues or groups of atoms, it is not obvious what
the convention should be (as the values are no longer directly comparable
to experiment). However, if we assume that "by residue" fluctuations from
experiment are agregates of atomic (mass weighted) fluctionations,
weighting by the mass seems appropriate so this is how I implemented it.

As I do not have a better answer, to delve further, you will need to dig
into the primary literature or hope for further responses here. Note that
the ptraj code (transformAtomicFluct() in actions.c) could be modified
to not do the mass weighting or to have the option...
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