[gmx-users] units of eigenvalues of mass-weighted covariance matrix

Tsjerk Wassenaar tsjerkw at gmail.com
Wed Jun 10 08:47:35 CEST 2009


Well, as has been pointed out before nm\S2\N stands for nm superscript
2 normal. That is correct for non mass-weigthed covariance analysis.
It's just fluctuation. Why would it be kg/m2 (kg/nm2) for mass
weighted? Look at the equations in the manual. It's
sqrt(mass)*sqrt(mass)*nm*nm, which makes something like kg m2, or
probably, in terms of Gromacs units, something like amu nm2. Work out
the math!


On Wed, Jun 10, 2009 at 4:16 AM, Mark Abraham<Mark.Abraham at anu.edu.au> wrote:
> Wang Qin wrote:
>> Dear all,
>>     I am confused on the units of the eigenvalues calculated from g_covar
>> of mass-weighted covariance matrix. From the output, it says the unit is
>>  "(nm\S2\N)" but from my understanding, it is supposed to be kg/m2.
> Various of the GROMACS analysis tools don't write the correct units in .xvg
> output. This looks like such a case. There's a section early in the manual
> that describes the GROMACS unit conventions, from which you
> should be able to deduce what the units are.
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
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