[gmx-users] reduced units

Justin Lemkul jalemkul at vt.edu
Tue Feb 12 02:18:46 CET 2013

On 2/11/13 6:15 PM, Pengzhi Zhang wrote:
> 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.

Using reduced units is far more straightforward from simple energy and 
coordinate output; their interpretation in g_covar is less clear.  I think the 
latter case is right, but you would have to go into the code to be sure.  The 
former case represents huge values of covariance which do not make any sense to me.



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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