[gmx-users] units for atomic coordinates in traj.xtc? nm?

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 25 13:28:24 CET 2011

Jennifer Williams wrote:
> A very quick question.
> Can someone confirm that atomic coordinates are stored as in the 
> traj.xtc file in units of nm (as opposed to Angstroms)?
> I am trying to figure out whether or not in the g_msd program reads in 
> nm or Angstroms. The standard output of the xy graph is nm2 and ps. I 
> can't see that the units are being divided by 10 in the g_msd code so I 
> am guessing the traj.xtc feeds in the units in nm.  Just want to be sure...

Standard units are given in Chapter 2 of the manual.  For distances, 
coordinates, etc everything is in nm.

You can also use gmxdump to convince yourself of this fact.


> Thanks


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


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