[gmx-users] reduced units

[Pengzhi Zhang]

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.

Sincerely,
Pengzhi

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

--
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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