damjanovic at uni-heidelberg.de
Thu Jul 2 00:05:24 PDT 2015
To whom it may concern,
I am trying to solve a problem that is more of mathematical nature, and
I would be very grateful if I could get any advice or pointers on how it
may be possible to do this (in Chimera or some other program I am not
I have a molecule that is more or less of cylindrical shape (quite
simple shape). I would need a way to surround this molecule with a
certain number of layers of solvent molecules that fit around the
surface of a cylinder (preferably 1 layer and then going up gradually).
The solvent molecules should be packed around the central molecule
efficiently (closest packing). An alternative way to approach this would
be to take a sphere made out of solvent molecules, put in the centre of
the sphere the one cylindrical molecule what is of interest, and let the
big sphere accommodate the new molecule. Also, for the sake of
simplicity, the solvent molecules can be approximated as small spheres
as well (their exact shape is not that relevant).
When this is done, all I would need is to get this file in a format like
cif, mol or gjf. I underline here that I am looking for a relatively
Could anyone please advise me on how to do something like this?
Thanks in advance and best wishes,
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