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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Scotland, with registration number SC005336.
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