[gmx-users] reduced units

Pengzhi Zhang pzhang5 at central.uh.edu
Mon Feb 11 23:02:22 CET 2013

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?


On 2/11/13 4:09 PM, Pengzhi Zhang wrote:
> Hello there,
> I'm a gromacs newbie. I am using gromacs function g_anaeig to do 
> principle component analysis. I use coordinates (converted to be .trr 
> files for
> gromacs) and topology from amber. I know that gromacs works with units 
> like nm, kJ/mol etc, while amber with angstrom. Does anyone know that 
> when gromacs read the coordinate files, whether it assumes the values 
> are in nm or in angstrom (if so, gromacs converts them by itself to nm 
> without telling us)?

Gromacs uses nm for everything except when a .pdb file is specified for
input or output, in which case Angstrom is used.



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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