[gmx-users] reduced units

Pengzhi Zhang pzhang5 at central.uh.edu
Mon Feb 11 23:26:00 CET 2013

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?


On 2/11/13 5:02 PM, Pengzhi Zhang wrote:
> Thanks Justin.
> I do use a .pdb file as the topology file, which is also in Angstrom, 
> not in full format of pdb though (basically atom index ,name and 
> coordinates). So in my case, gromacs will read all the coordinates in 
> angstrom? Thus I need to ignore the units nm in output .xvg files. Do I
understand it correctly?

No.  There is no magic done here.  If you provide a .pdb file as input or
output to any Gromacs program, that program understands that .pdb files use
Angstrom and it processes the coordinates appropriately.  All Gromacs tools
read and write nm by default, including trajectories (.trr and .xtc) as well
as output files from analysis tools (.xvg and others).



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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