[gmx-users] reduced units

Justin Lemkul jalemkul at vt.edu
Mon Feb 11 23:06:21 CET 2013

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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