[gmx-users] reduced units

Pengzhi Zhang pzhang5 at central.uh.edu
Tue Feb 12 00:15:08 CET 2013

In my case, all the related units are about length, so I won't consider
temperature, charge etc. 

Here is the confusion.

On one hand, from the above discussion: If the input is from the .pdb file,
which is in reduced units ( {\sigma}=3.8 Angstrom), as well as the
coordinate file, the program g_covar reads the coordinates in Anstroms and
convert them to nms, then gives an output of all the eigenvalues of the
covariance matrix, in units of nm^2, for example, the first eigenvalue given
is 5.5 nm^2. So mapping to the correct reduced units, I think I need to
change the nm^2 to ({\sigma}*10)^2=1444 Angstrom^2, thus the first
eigenvalue is 550 {\sigma}^2, i.e. 7942 Angstrom^2.

On the other hand, per to the manual, the output should be anyway 5.5
{\sigma}^2 although written in 5.5 nm^2 in the .xvg file, as if gromacs does
no unit-conversion here at all, even a .pdb file is given as input.

The latter gives values of better sense from my actual example.


On 2/11/13 5:26 PM, Pengzhi Zhang wrote:
> Justin, I'm a little confused again. Let me put it in a more general 
> way. If I used everything in .pdb and .trr files in reduced units 
> {\sigma}, then gromacs will assume them are in Angstroms, and output 
> in nms (by dividing the input values by 10). That means, the real unit 
> for the output is {\sigma}*10. Is it correct?

If your input is in reduced units, then so too is the output, per manual
section 2.3.  Perhaps you can provide an actual example of whatever is
causing your confusion.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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