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 -- ======================================== 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 ======================================== -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists