[gmx-users] Conversion of units to nm in .xyz or pdb

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 30 01:20:38 CEST 2009

Jennifer Williams wrote:
> hello gromacs users,
> I am working with a silica structure which is parallepiped in structure, 
> i.e the unit cell is
> 46.4207   37.7846  18.9596 angles =90, 90, 120
> I have a structure file in .xyz and .pdb but the units are in Angstroms 
> and for gromacs I assume that I need to convert these units to nm? This 
> is where I am encountering problems.

You do not need to make any conversion.  Gromacs can handle .pdb files just fine.

> I have tried simply dividing the atomic coordinates and cell lengths by 
> a factor of 10 but the resulting structure doesnt look right in vmd. Do 
> I need to use some sort of symmetry transformation to take the non-cubic 
> symmetry into account when scaling the coordinates? Is there some 
> program (either within gromacs or external) which will convert atomic 
> coordinates from Angstroms to nm while carrying out the necessary 
> symmetry operations?

Simply dividing by 10 may have altered the formatting of your file.  There are 
certain formatting standards that must be adhered to in structure files.  But as 
I said above, .pdb format is just fine.


> 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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