[gmx-users] reduced units

Justin Lemkul jalemkul at vt.edu
Mon Feb 11 22:45:01 CET 2013

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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