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

[Jennifer Williams]

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.

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?


Thanks





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